DNA Analysis Research Articles

Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples.

The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 102 copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.IMPORTANCEPrevious studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.

Genetic and Haplotype Diversity of Clarias gariepinus (Burchell 1822) Based on Cytochrome c Oxidase I (COI) Gene

The evaluation of mitochondrial DNA and genetic analysis is helpful for economically significant species. Clarias gariepinus is a critical species in aquaculture. This study investigates the genetic diversity and population differentiation of C. gariepinus from 19 countries using 164 sequences of the mitochondrial DNA’s Cytochrome c oxidase I (COI) gene. The haplotype analysis revealed a total of 17 haplotypes, with a nucleotide diversity (π) of 0.012 and a haplotype diversity (Hd) of 0.87. The results of an AMOVA and fixation index indicated significant genetic variation and structure among the populations. Additionally, neutrality tests and mismatch distribution analysis supported the hypothesis of under-purifying selection in C. gariepinus. The findings suggested that the population did not experience expansion. In conclusion, the genetic analysis highlighted substantial variation among C. gariepinus populations from different locations, providing valuable insights for the global management of this species.

Heat exposure promotes sarcopenia via gut microbiota-derived metabolites.

The unprecedented rise in global ambient temperatures in the last decade has significantly impacted human health, yet how heat exposure affects the development of sarcopenia remains enigmatic. Here, we demonstrate that chronic heat exposure induces skeletal muscle volume loss, leading to muscle strength and functional decline in mice. The microbiota composition of heat-exposed mice was analyzed using 16S ribosomal DNA analysis. Liquid chromatography-mass spectrometry (LC-MS) was used to explore the effects of heat exposure on the blood metabolome and to further analyze the correlation between blood metabolism and gut microbiota. Transplantation of microbiota from heat-exposed mice to germ-free mice was sufficient to increase adverse effects on skeletal muscle function in the host. Mechanistically, using an untargeted metabolomics strategy, we reveal that altered gut microbiota due to high temperatures is associated with elevated serum levels of homocitrulline. Homocitrulline causes mitochondrial dysfunction in myocytes by exacerbating ferroptosis levels. And Nrf2 activator (Oltipraz) supplementation alleviates muscle atrophy and dysfunction induced by heat exposure. Our findings reveal the detrimental effects of heat exposure on muscle function and provide new strategies for treating sarcopenia.

SNP Genotype Imputation in Forensics—A Performance Study

Background/Objectives: Emerging forensic genetic applications, such as forensic investigative genetic genealogy (FIGG), advanced DNA phenotyping, and distant kinship inference, increasingly require dense SNP genotype datasets. However, forensic-grade DNA often contains missing genotypes due to its quality and quantity limitations, potentially hindering these applications. Genotype imputation, a method that predicts missing genotypes, is widely used in population and medical genetics, but its utility in forensic genetics has not been thoroughly explored. This study aims to assess the performance of genotype imputation in forensic contexts and determine the conditions under which it can be effectively applied. Methods: We employed a simulation-based approach to generate realistic forensic SNP genotype datasets with varying numbers, densities, and qualities of observed genotypes. Genotype imputation was performed using Beagle software, and the performance was evaluated based on the call rate and imputation accuracy across different datasets and imputation settings. Results: The results demonstrate that genotype imputation can significantly increase the number of SNP genotypes. However, imputation accuracy was dependent on factors such as the quality of the original genotype data and the characteristics of the reference population. Higher SNP density and fewer genotype errors generally resulted in improved imputation accuracy. Conclusions: This study highlights the potential of genotype imputation to enhance forensic SNP datasets but underscores the importance of optimizing imputation parameters and understanding the limitations of the original data. These findings will inform the future application of imputation in forensic genetics, supporting its integration into forensic workflows.

Rapid response Task Force: addressing the detection of Aedes albopictus in Lisbon, Portugal

Abstract Issue The invasive Aedes albopictus mosquitoes are spreading in southern Europe and pose a heightened risk of mosquito-borne diseases, like Dengue and Chikungunya. On September 2023, A. albopictus was first identified in Lisbon through community-based surveillance and a multidisciplinary national Task Force (TF) was convened. Description of the problem The TF included experts in epidemiology, entomology, environmental health, laboratory diagnosis, prevention and control and communication. The objectives were to i) confirm A.albopictus presence in Lisbon and adjust the risk assessment, ii) raise awareness and prevent mosquitoes’ spread, iii) revise national guidelines on arboviruses surveillance and control. During September-December 2023, the National Network for Vectors Surveillance (REVIVE) and the Hygiene and Tropical Medicine Institute sampled mosquito-prone habitats within 2km-radius of the detection point using QGIS software. They used snowball sampling to identify any new foci. They placed ovitraps for ongoing surveillance and conducted morphological analysis and xenomonitoring for pathogen DNA and RNA detection at the national reference laboratory. Results By November 2023, A.albopictus was detected in two new foci. No mosquitoes tested positive for arboviruses, and no autochthonous cases of mosquito-borne diseases were identified. The TF developed national guidelines for vector prevention and control and awareness for arboviruses and trained municipality workers. To raise awareness, we communicated with experts and the public through existing channels and media. As of April 2024, no new foci have been detected. Lessons Community-based surveillance and REVIVE approach were crucial for invasive A.albopictus detection and monitoring in Lisbon. Rapid multidisciplinary TF coordination may have been key for timely vector control.

Multi-omics integration analysis identifies pathogenic candidate genes of congenital heart defects with vascular malformation

Abstract Background Congenital heart defects (CHD) with vascular malformation harbors numerous genetic and epigenetic aberrations of DNA copy numbers and methylation. Proteomic deregulation by the aberrations plays key driver roles in heterogeneous progression of CHD. However, it still remains largely unknown about integrative analysis of genetic, epigenetic regulation and proteome in CHD. Purpose We employed a multi-omics approach to explore pathogenic candidate genes in CHD with vascular malformation. Methods Previously, we gathered WES data for 216 CHD patients with vascular malformation and 100 healthy controls. Meanwhile, we carried out DNA methylation analysis from 11 patients and 5 controls. Here, we profile proteomics of vascular tissues from 11 patients and 5 controls. Integration analysis of DNA copy-number-correlated (CNVcor) genes, methylation-correlated (METcor) genes and differentially proteins reveal the innovative and crucial pathogenetic genes. We then detected spatiotemporal expression patterns of candidate genes in zebrafish embryos using in situ hybridization and qPCR, and verified the roles in vascular development by morpholino-mediated gene knockdown. Results 90 differentially expressed proteins (DEPs) were obtained using proteomics and were mainly related to cell adhesion and migration, angiogenesis, amino acid metabolism, and HIF-1 signaling pathway through GO and KEGG pathway enrichment analysis. 15 hub proteins were identified by WGCNA analysis (Fig 1). Additionally, we found that the frequencies of the aberrancies of the CNVcor genes were significantly correlated with the METcor genes (Fig 2 C). We obtained 1924 differentially CNVcor genes and 952 differentially METcor genes. Then, we computed the Pearson’s correlation coefficients of all three-omics by pairwise comparison and found that the distribution of correlations was bimodal (Fig 2 D). Meanwhile, 28 overlapped genes were observed among three-omics. We screened out 11 candidate genes (TIMP1, BGN, LTBP1, AKR1C3, LOXL3, MAOA, MAOB, GNA12, IFI30, CNTNAP1, IGF2BP1) according to the node degree of PPI network analysis between 28 genes and known vascular development related genes. We further figured out LOXL3, MAOA, CNTNAP1 and IGF2BP1 are the novel important genes for vascular malformation, of which CNTNAP1 is the joint gene of three-omics. Through expression patterns and gene knockdown in zebrafish embryos, we revealed that LOXL3, MAOA, CNTNAP1 and IGF2BP1 affect vascular development (Fig 2 E-G). Conclusions We identify novel key candidate genes (LOXL3, MAOA, CNTNAP1 and IGF2BP1) potentially related to CHD with vascular malformation and elucidate the possible molecular pathogenesis of CHD. Our multi-omics integrative analysis provides new insights on the multi-layered etiology of CHD, which might be helpful in developing clinical diagnosis and precaution for CHD.Figure 1Figure 2

Telomere length across spectrum of metabolic health

Abstract Introduction Telomere length is a marker of cellular aging and is correlated with various cardiovascular risk factors. Aim To assess the association between obesity, metabolic syndrome (MetS) and telomere length. Methods The LIPIDOGEN study was carried out in the primary care 2015. Patients recruited to LIPIDOGEN cohort (n=1788) were a random subset of patients from LIPIDOGRAM 2015 (n=13,724) study. Patients for LIPIDOGRAM2015/LIPIDOGEN study were recruited in all 16 administrative regions in Poland and physicians were proportionally distributed to the number of inhabitants in each administrative region. Each patient was asked to fill the questionnaire on risk factors, chronic diseases, treatments and lifestyle and also had saliva secured for DNA analyses. Recruited patients were divided into four groups based on the presence of MetS: 1) HS – healthy slim 2) MHO – metabolically healthy obese 3) NOMS – Non-obese with MetS 4) MUO – metabolically unhealthy obese. MetS was diagnosed basing on Joint Interim Statement 2009 criteria. Relative telomere length (rTL) was measured using quantitative polymerase chain reaction. Results DNA quality was sufficient for further analyses in 1606 patients. After removing of outliers, 1342 patients (Females - 59.3%, mean age- 50.2 years) were included for further analyses (HS-488, MHO-180, NOMS-165, MUO-509). Increase in BMI, waist circumference, frequency of diabetes mellitus, hypertension, dyslipidemia and history of myocardial infarction moving from HS to MUO was observed. (Table 1.). MUO group exhibited the highest triglycerides and lowest HDL-C levels. RTL length, an indicator of cellular aging, was inversely correlated with metabolic health, being shortest in the NOMS and MUO groups, which may indicate a link between metabolic health and accelerated biological aging. Conclusions Telomere length is shorter in patients with obesity as compared to lean patients even without the presence of MetS. Telomere length in patients with MetS, regardless of concomitant obesity, is shorter than in patients without MetS. Figure 1. Telomere length across metabolic health categories. Table 1. Clinical characteristics of the study participants.Figure. 1.Table. 1.

Biomarkers in Colorectal Cancer: Actual and Future Perspectives

Biomarkers in colorectal cancer (CRC) are of great interest in the current literature due to improvements in techniques such as liquid biopsy and next-generation sequencing (NGS). However, screening methods vary globally, with multi-target stool DNA (mt-sDNA) predominantly used in the USA and, more recently, the Cologuard Plus; biomarkers such as the Galectins family and septins show promise in early detection. Gut microbiome assessments, such as Fusobacterium nucleatum, are under intense exploration. Diagnostic tests, such as circulating DNA analysis via NGS, exhibit effectiveness and are being increasingly adopted. Circulating tumor cells emerge as potential alternatives to traditional methods in terms of diagnosis and prognosis. Predictive biomarkers are well established in guidelines; nonetheless, with the aid of machine learning and artificial intelligence, these biomarkers may be improved. This review critically explores the actual dynamic landscape of CRC biomarkers and future, promising biomarkers involved in screening, diagnosis, and prognosis.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Punjab Tar-1: A New Short Duration, High Yielding and Disease Resistance Long Melon Variety (Cucumis melo) Released in Pakistan.

The development of new crop varieties with favorable features is a continuing effort. With the passage of time, a cultivated variety becomes subjected to various biotic and abiotic plant stresses. This article describes development of an innovative and imaginative long melon cultivar called "Punjab Tar-1."This article discusses creation of a novel and inventive long melon variety known as "Punjab Tar-1." Current long melon varieties in Pakistan are sensitive to climatic conditions and susceptible to pest and disease attack. A New Short Duration, High Yielding and Disease Resistance Long Melon Variety (Cucumis melo) is released in Pakistan to address these current issues of long melon varieties A high yielding and early maturing variety of long melon “Punjab Tar-1” has been developed by Vegetable Research Institute, Faisalabad, Pakistan through mass selection. Plants were selected from an open pollinated indigenous source population with main emphasis on earliness, fruit shape, color and taste and yield. Selection intensity was 15% in 1st three selection cycles and 30% in subsequent four selection cycles whereas yield trials were started from 8th selection cycle. The fruit of this variety has a strong longitudinal rib that makes it difficult for eating by caterpillars. This variety has wide adaptability and exhibits stable yield across multiple environments. Notably, "Punjab Tar-1" contains 10.59 % crude protein and 1.08% crude fat content. Genetic uniformity and distinctiveness of this variety was confirmed through SSR polymorphism. Punjab Tar-1 variety has been approved by Punjab Seed Council in its meeting held on 2021 and was recommended for general cultivation in Punjab, Pakistan. Its certified seed is available for farmers at Vegetable Research Institute, Faisalabad. This newly approved variety will aid to save the precious foreign reserves by reducing vegetable seed import bill. In Pakistan, seed market of long melon is occupied by improved varieties. In multi-location evaluation, one said variety has exhibited high yield and stability than exotic germplasm. This is the first variety developed in Pakistan having good taste, early maturity, long shape, and high yield potential. DNA fingerprinting has further confirmed that it is distinct from local material, having novelty and diversity.

DNA profiling, nutritional value and phytochemical investigation of Cissus rotundifolia Lam. growing in Yemen

Cissus rotundifolia Lam. (Vitaceae) is a wild plant that is commonly used as food and medicine. There are limited studies on the phytochemical composition of this plant. So, this study aims to investigate C. rotundifolia growing in Yemen phytochemically. HPLC analysis of C. rotundifolia aerial parts led to the identification and quantification of four compounds (isoorientin, quercetrin, quercetin, and linarin), among which isoorientin and quercetrin were the major. Proximate analysis showed high fibre content and low moisture content, whereas the nutritional values showed a high carbohydrate content which gave rise to higher nutritional value (266.39 Kcal.). Potassium, calcium, iron, magnesium, and vitamin E were present in high concentrations. Investigation of the methylene chloride and n-butanol fractions lead to the isolation of seven compounds: β-sitosterol, magnificol, β-sitosterol-glucoside, quercetin, quercetrin, isoorientin, and linarin. This is the first report on isolating these compounds from the investigated plant.

A multidisciplinary approach to forensic biological profiling on a single tooth and nail sample.

Analysis of a single tooth and nail can provide valuable forensic information, including year of birth, year of death, age, sex, DNA-profile, geographic residence during childhood and at time of death and drug exposure. The aim is to minimize the amount of used bodily material and to validate the applicability of a multidisciplinary sampling protocol. A nail of the big toe, a tooth and blood of seven deceased individuals were collected postmortem. Collected materials were sampled and segmented in accordance with the multidisciplinary sampling protocol. DNA analysis was conducted on the pulp of the tooth, isotope analysis (Sr, Pb, O and C) on the enamel and 14C-, toxicological and tooth cementum annulation analysis on root segments. DNA-, isotope (Sr, Pb, O and C) -, toxicological-, and 14C -analysis were conducted on toenail segments. The acquired DNA profiles were compared with profiles acquired from blood. Material from seven deceased persons was analysed. 45 out of 56 analyses on dental samples were successful, constituting a success rate of 80%. Additionally, 27 out of 35 analyses were successful on nail samples, yielding a success rate of 77%. DNA-, toxicological and 14C- analyses performed better in nail than in tooth. Isotope analyses performed better in tooth than in nail. A profile with personal characteristics was constructed and matched for 62% of parameters with collected medical information. The performed sampling protocol for simultaneous multidisciplinary forensic analysis on a single tooth and nail sample provided applicable results and valuable information.

Population genomics of a specialized insect, Tetraopes texanus (Coleoptera: Cerambycidae), across a fragmented grassland system

AbstractSpecialist insects are especially susceptible to loss of genetic diversity in the face of habitat destruction and fragmentation. Implementing effective conservation practices for specialist insects will benefit from knowledge of population structure and genetic diversity. Because insects are hyper-diverse, characterizing the population structure of all species within the insect community is untenable, even if focused within a particular habitat type. Thus, concentrating on a single species specialized to a particular habitat type is needed to infer general trends. Here, we investigate the range-wide population genetics of Tetraopes texanus Horn 1878 (Coleoptera: Cerambycidae), which provides a useful model of grassland insects due to its’ habitat specificity and unique biology. Tetraopes texanus occurs primarily in Texas and Oklahoma, into Northern Mexico, and possibly into eastern New Mexico but also occurs in Black Belt prairies of Mississippi and Alabama. Mitochondrial and nuclear DNA (RAD-seq) analysis identified two distinct population clusters of T. texanus corresponding to the Texas and Oklahoma population and the Mississippi and Alabama population. Demographic models indicate ongoing, though incomplete, isolation of the two populations, with estimated dates of divergence in the mid-Pleistocene, coinciding with the end of a glacial period and a shift in glacial interval. These results can inform conservation of grassland adapted insects and offers insight to the biogeography of the Gulf Coastal Plain.

Influence of Early Life Factors on the Breast Milk and Fecal Microbiota of Mother–Newborn Dyads

Maternal gut and breast milk (BM) are key in vertically transmission bacteria to infants, shaping their gut microbiota in early life. Although the establishment of early gut microbiota is known, the role of the combined influence of maternal factors and newborn characteristics is not explored. In this study, we aimed to assess the influence of maternal BMI and total body fat, age, delivery mode, and newborn sex on the diversity and composition of the BM and gut microbiota (GM) in mother–newborn dyads. In this cross-sectional study, of the 986 pregnant women candidates, 53 participated, and, finally, 40 mother–newborn dyads exclusively breastfeeding at 20–28 days postpartum were included. Metataxonomic profiling of DNA extracted from BM and fecal samples was conducted using 16S rRNA sequencing. Globally, the findings offer valuable insights that excessive adiposity, age, and C-section delivery influence a lower abundance of specific taxa in the BM, maternal gut, and gut of newborns. Also, the simultaneous analysis of maternal factors and newborn characteristics shows that maternal age and newborn sex explain an important variation in the microbiota composition. These results add to the understanding of the intricate interplay between maternal factors and the microbial communities that influence early-life gut and BM microbiota.

Evaluation of Multi-antibiotic Resistance Index (MAR) and Molecular Characterization of Pseudomonas aeruginosa Isolated in Pathological Products from Chad

Pseudomonas aeruginosa is a bacterium present in several ecological niches causing opportunistic infections in humans. In developing countries like Chad, this bacteria is responsible for various human pathologies. High-priority pathogens, such as Salmonella and Shigella, represent a particularly heavy burden in low- and middle-income countries, as do Pseudomonas aeruginosa and Staphylococcus aureus, which pose serious problems in health centers. The objective of this study was to evaluate the multi-antibiotic resistance index and to carry out a molecular characterization of Pseudomonas aeruginosa isolated in pathological products from Chad using by rep-PCR (GTG)5. Antibiotic resistance phenotypes were obtained by interpreting the results of our previous study on antimicrobial resistance of Pseudomonas aeruginosa isolated from human infections in N'Djamena, Chad. In this study, two phenotypes were obtained that is XDR and MDR. Thus, 24/36 of strains came from urine and 29/36 strains were MDR. The multi-antibiotic resistance (MAR) indexes varied from 0.33 to 0.86. The rep-PCR allowed good discrimination of Pseudomonas aeruginosa strains in this study. These isolates were grouped based on characteristic bands appearing in their genetic fingerprint profiles. In this study, Pseudomonas aeruginosa strains isolated from urinary tract infections and pus were classified as XDR and MDR type strains.

Among the world's smallest vertebrates: a new miniaturized flea-toad (Brachycephalidae) from the Atlantic rainforest.

The genus Brachycephalus includes miniaturized toadlets with two distinct morphotypes: brightly colored species with a bufoniform phenotype and smaller, cryptic species with a leptodactyliform phenotype. The diversity of leptodactyliform species is still underappreciated, and we generally lack fundamental information about their biology. Recent sampling efforts, including DNA analyses and recordings of advertisement calls, have improved our understanding of this group. In the present study, we describe a new species of Brachycephalus, one of the smallest vertebrates known. This new species is distinguished from its congeners by a combination of morphological, bioacoustic, and genetic data. Despite being among the smallest frogs globally (the second smallest amphibian species), it exhibits skeletal traits typical of larger frogs, such as the presence of cranial bones that are lost or fused in other miniature frogs, including other Brachycephalus. Our description underscores how new discoveries within the megadiverse fauna of the Atlantic Forest-a rich biodiversity hotspot-can provide insights into phenotypic variation, including vertebrate body size. By describing this new species, we also aim to revisit the hypothesis that the type series of B. hermogenesi includes two species, potentially including individuals of the species described here.

Effects of Dietary Protein Levels, Net Energy Levels, and Essential Amino Acid-to-True Protein Ratios on Broiler Performance

Supplementing essential amino acids (EAAs) without considering non-EAA (NEAA) and energy contents in reduced-crude protein (CP) diets may alter EAA-to-true protein (E:T) and energy-to-protein ratios, potentially compromising growth. This study aimed to evaluate the effects of CP, E:T, and net energy (NE) on broiler performance. The treatments were as follows: T1—reduced CP (16%, RP), low NE (9.9 MJ/kg, LNE), low E:T (0.56, LE:T); T2—RP, LNE, high E:T (0.60, HE:T), with imbalanced EAA (excess Met and deficient Thr); T3—RP, high NE (10.4 MJ/kg, HNE), LE:T; T4—RP, HNE, HE:T; T5—normal CP (18%, NP), LNE, LE:T; T6—NP, LNE, HE:T; T7—NP, HNE, LE:T; and T8—NP, HNE, HE:T. The study employed as-hatched Cobb 500 broilers in two experiments. Exp.1 studied the broiler performance from d19 to 35, with eight replicates per treatment and 16 birds per replicate (n = 1024). Birds were randomly assigned to different treatments, and at the end of their lives, all were dissected to determine their sex and account for any gender-related effects. Exp.2 measured NE values in respiration chambers from d25 to 28, with six replicates per treatment, and two birds (a male and a female) per replicate (n = 96). The bird gender was determined through high-resolution melting curve analysis of feather DNA. The measured NE values were used to calculate NE intake (NEi) in Exp.1. The results showed that T4 improved (p < 0.001) weight gain (WG), feed conversion ratio (FCR), and NEi relative to T1, T2, and T3, and protein efficiency (WG/CP intake) relative to all treatments. The live performance (feed intake, WG, FCR) and NEi of birds fed T4 reached a level equal to those of birds fed NP diets (T5 to T8). These results suggest that a dietary E:T ratio of 0.60 is necessary to maximize nutrient utilization and to restore growth rate in broilers fed RP diets.

A haplogroup-based methodology for assigning individuals to geographical regions using Y-STR data

Y chromosome markers are essential tools in forensic genetics, offering valuable insights for genetic identification. This study seeks to develop a forensic prediction model using machine learning techniques to improve the efficiency of genetic identification processes. Specifically, the model aims to predict an individual's nearest geographical area of residence based on Y chromosome marker analysis. The methodology involved four key steps: haplogroup determination, primary branch identification, geographical region assignment, model stratification, and fine-tuning. Once developed, the model can be integrated into decision support systems, providing forensic geneticists with a reliable knowledge source to enhance decision-making during investigations.

Genetic variability and discriminatory power of RM Y-STRs in gilgit men: a population study

AbstractShort Tandem Repeats (STRs) found on the Y chromosome have multiple applications, such as in forensic investigations, male identification for legal reasons, as well as population genetics. However, commercially accessible Y-STR tests are limited in their capability to distinguish closely linked male individuals in forensic genetics. Recent studies have revealed that Rapidly Mutating Y-STRs (RM Y-STRs) offer significantly greater haplotype diversity around the worldwide populations associated to conventional Y-STRs, though some RM Y-STR loci are not contained, current commercial kits. The objective of this research is to create a database of RM Y-STR haplotype frequencies for the Gilgit population in Pakistan and evaluate the effectiveness of these genetic markers in distinguishing individuals with genetic variations. The research involved examining several RM Y-STRs in 56 unrelated Gilgit men. The statistical analysis determined that the majority of the loci-maintained haplotype values, as specific varied in certain cases. The results presented that the RM Y-STRs were very effective in distinguishing genetic changes among the Gilgit population, through a GD value of 0 for DYD403S1 and GD values greater than 0.7 for all other loci, with maximum value of 0.9920 for the RM Y-STR DYS612.

Zooarchaeological and ancient DNA identification of a non-local gopher tortoise (Gopherus polyphemus) in New Orleans, Louisiana, USA

Zooarchaeological and ancient DNA identification of a non-local gopher tortoise (Gopherus polyphemus) in New Orleans, Louisiana, USA