DNA Analysis Research Articles

Nanopore sequencing in surveillance of fungicide resistance

By detecting plant pathogens as early as possible, swift action can be taken to mitigate the spread of disease. Monitoring fungicide is another key part of effective disease control as pathogens can develop resistance to fungicides, rendering them ineffective. The area of plant disease management is advancing apace thanks to innovative research incorporating technical advances in detection and monitoring. For example, Dr Semcheddine Cherrad, Research and Development Manager at Conidia Coniphy, is conducting innovative studies on microbiological assessment and contamination control. The research team at Conidia Coniphy has been working on the detection of plant pathogens and monitoring of fungicide resistance for over 15 years and the teamâ–™s collective efforts in bioassay and molecular analysis, combined with the adoption of new technologies and processes is overcoming challenges in the field. For example, the researchers are utilising new generation sequencing (NGS) with long-read sequencing to generate huge datasets on DNA molecules of genes coding for proteins targeted by fungicides. The team has developed a tool for mould identification called ID-Fungi Plates (IDFP). It is a user-friendly medium that accelerates the identification of fungal pathogens by Maldi-tof. They have also developed a software called FUNGI MESURE, which can quantify fungal spores in samples, providing an accurate overview of fungal measures and facilitating lab routine tasks of methods with fungi. In addition, a database established by the team called FUNGI DNA supports the identification and study of fungal strains through DNA analysis.

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

On Accountability: Genetic Tools for Justice and Injustice in Criminal Proceedings

Analysis of DNA found at crime scenes has made headlines when used to solve serial killer cold cases. The DNA Identification Act of 1994 approved the Combined DNA Index System (CODIS), a database that stores profiles of 20 genetic markers for forensic investigations. The CODIS markers were specifically chosen because they were thought to be unlinkable to personally identifiable individual traits. However, advances in genetics research have expanded the traits associated with CODIS markers and increased the tools and applications of forensic genetics, thus further increasing the information investigators could gain from a suspected person’s CODIS profile. This is also true regarding private companies, who may analyze genetic information beyond that included in a CODIS profile. These scientific developments may lead to infringements on genetic privacy rights. Additionally, in 2013, the US Supreme Court held in Maryland v King that people who have been arrested, even if they are acquitted or never indicted, can be added to CODIS databases. Due to racial biases in policing and arrests, this has led to inequity in who is represented in CODIS databases, specifically an over-representation of Black individuals’ genetic profiles. Therefore, the use of genetic tools in criminal proceedings, including but not only from CODIS databases, pose risks to privacy and also serve as a seemingly race-neutral tool that, in practice, promotes racial inequity. We suggest implementation of state-specific research and oversight boards with three charges focused on CODIS and investigations using genetic tools employed by private companies: (1) study uses of genetic tools in criminal investigations; (2) study the impact of genetic tools in criminal proceedings and interface with stakeholders and the general public; and (3) use knowledge from (1) and (2) to inform policy recommendations, for which we make several initial suggestions. These boards will provide accountability to increase accuracy, privacy, and equity when using genetic tools in criminal proceedings.

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.

Characterisation of identity-informative genetic markers in the Australian population with European ancestry

Identity-informative single nucleotide polymorphisms (iiSNPs) are valuable genetic markers for human identification and kinship testing in forensic casework, especially when the quality and quantity of DNA evidence is not suitable for routine short tandem repeat (STR) profiling. This study analysed 105 buccal samples representing the Australian population with European ancestry in order to assign allele frequencies and conduct population genetic analyses for 94 iiSNPs and 20 STRs. The markers were assessed by calculating relevant forensic statistics and testing for deviations from Hardy-Weinberg and linkage equilibrium. No linkage of statistical significance was observed between any of the pair-wise combinations of the combined 114 identity-informative markers and only one STR exhibited deviation from Hardy-Weinberg equilibrium (D8S1179). The probability of matching genotypes being observed within this population was of the order of 10−23 for STRs, 10−38 for iiSNPs and 10−60 for the combined identity-informative marker panel, improving the ability to discriminate between individuals when calculating likelihood ratios in direct or indirect matching scenarios. Further, the addition of iiSNPs will facilitate identifications when suboptimal STR profiles are recovered from compromised or challenging samples and aid comparisons to genetic relatives for familial or kinship testing.

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.

Mass spectrometry-based proteomics for source-level attribution after DNA extraction

Biological traces recovered from crime scenes serve as vital evidence in forensic investigations. While DNA evidence is frequently used to address the sub-source level of the hierarchy of propositions, the biological source of the DNA can be highly probative at the source level. Current body fluid detection methods pose certain limitations, such as reports of false positive results from some of the presumptive and/or confirmatory tests in current use. These tests are also individual tests for the detection of one body fluid, meaning that if the sample is suspected to be a mixture of multiple body fluids, then different tests would need to be conducted to confirm the body fluid(s) present, which may exhaust small amounts of available biological trace. Proteomics applications for the identification of body fluids have been previously explored, and potential biomarkers indicative of body fluids discovered from liquid-chromatography tandem mass spectrometry (LC-MS/MS) methods have been reported. This work focuses on developing a mass spectrometry-based proteomics approach for the identification of body fluids by targeting discriminating peptide biomarkers from the non-DNA component left over after DNA extraction of samples. The non-DNA component is typically a waste product but with unappreciated evidential value. Our methodology for the purification of proteins from the post-DNA extraction waste includes an acetone precipitation and single-pot solid-phase-enhanced sample preparation (SP3) technique, microwave-assisted trypsin digestion, and LC-MS/MS analysis of the resultant peptides. Preliminary results from this proof-of-concept study include a list of potentially discriminating proteins and peptides for blood, saliva, and semen developed from the analysis of post-DNA extraction waste. Our method allows for multiple analytes to be targeted simultaneously from a DNA profiling waste stream and we anticipate that it could eventually be incorporated into standard forensic laboratory workflows.

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.

Structural Characterization of DNA from Allium Leaves and E. coli by Surface-Enhanced Raman Spectroscopy (SERS)

The label-free detection of biological molecules was demonstrated for different types of DNA. Surface-enhanced Raman spectroscopy (SERS) investigation on nucleic acids extracted from leaves of different Allium cepa cultivars (cvs.) De Buzău, Aurie de Buzău, Rubiniu, Roşie de Arieş as well as taxa A. ursinum, A. senescens subsp. montanum, A. schoenoprasum, A. obliquum, and A. fistulosum was performed using 532-nm laser excitation. Main SERS vibrations of these nucleic acids have been characterized, highlighting those at 658, 704, 1089, and 1125 cm−1 attributed to dG and dA phosphodiester groups as well as deoxyribose, specific constituents of DNA. The mild basic pH conditions of the samples can induce a partial breaking of the hydrogen bonds from the dsDNA, which affects the A = T/T = A as well as C≡G/G≡C base pairs and causes the aggregation of AgNPs mixed with DNA of the Allium cultivars and species. Also, SERS profiles of genomic DNA from E. coli 1559 were analyzed at decreasing pHs from 7 to 4. Protonation of the nitrogen N3 of the aromatic six-membered ring of both deoxyadenosine and deoxyguanosine, respectively, induces the decrease of the peak’s intensity at 1588 cm-1. Furthermore, SERS characteristics of plasmidic DNA from E. coli 7832 and of chromosomal DNA from E. coli MG 1655 are provided, with specific SERS modes indicated and new SERS bands found upon nucleic acids in vitro aging. Principal component analysis (PCA) in the full SERS spectrum range of bacterial DNA was performed.