DNA Analysis Research Articles

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.

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

Association between forensic DNA and odontology in human identification during mass disaster: a systematic review

BACKGROUND: According to the literature, forensic odontology is one of the most effective and affordable scientific techniques for identifying victims of mass disasters. This research methodically reviews the role and function of forensic odontologists in several global mass disasters. Forensic DNA in odontology is associated with the importance of its application in the identification of humans of mass disasters. As the crime rate continues to rise, the field of forensic medicine has evolved significantly. Forensic dentists play a pivotal role in various areas of crime scene investigations, thereby helping solve innumerable mysteries. AIM: The study aimed to increase the body of knowledge for future research on forensic odontology by conducting a systematic review search to investigate possible forensic DNA in odontology associated with the importance of its application in the identification of humans of mass disasters. MATERIALS AND METHODS: Six databases, including Google Scholar, PubMed, Scopus, Embase, Web of Science, and ScienceDirect, were analyzed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) quality scale. The literature search, conducted until February 2024, informed important research choices. RESULTS: A total of 16 (100%) studies related to forensic DNA of mass disasters were identified. Of these, only seven (43.75%) articles related to dental DNA were included in this review. Of the 4,808 articles obtained, 138 duplicates or irrelevant articles were eliminated. Following a full-text review, seven studies were selected based on eligibility criteria. The highest percentage of victims was identified using dental DNA. In a few studies, some samples were insufficient for complete DNA profiling due to factors such as the method of DNA extraction. CONCLUSION: Forensic odontology has played a significant role in the identification of victims of several mass disasters around the world. Although teeth are an excellent source of DNA for humans, future studies with larger sample sizes, appropriate control groups, and standardized techniques of DNA extraction need to be conducted.

Reasons for Potential Unreliability of DNA Evidence: A Critical Examination

DNA evidence is widely regarded as the "gold standard" in forensic science because of its capacity to accurately identify individuals and exonerate the innocent. However, several factors cast doubt on its reliability in criminal investigations. This study offers a comprehensive exploration of critical issues influencing the trustworthiness of DNA evidence, including errors in evidence collection, overlooking additional DNA samples at the crime scene, the absence of credible witnesses during searches, and the lack of video documentation throughout the processes of seizure, transportation, and lab analysis. Other concerns include human errors, inconsistent DNA analysis protocols among forensic laboratories, and potential contamination during sample collection. Furthermore, the research delves into laboratory errors, subjective interpretations, and existing biases. There is an increasing worry regarding the excessive reliance on DNA evidence without sufficient investigative corroboration, along with the potential misinterpretation of statistical probabilities by jurors. The article also examines ethical issues surrounding the expansion of DNA databases, privacy violations, and familial DNA searches. Citing pivotal academic studies and landmark legal cases like those of O.J. Simpson and Amanda Knox, this analysis highlights the pressing need for rigorous standards to govern the ethical use of DNA evidence in the criminal justice system.

Fetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus.

The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects. Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase activity gene expression ( bsh ), abundance of certain bile acids, and hepatic expression of Slc10a1 . In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome- associated differences in methylation of 196 loci in total, 176 of which show conserved profiles between mother and offspring. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

A cry for kelp: Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae.

Genomic resources have yielded unprecedented insights into ecological and evolutionary processes, not to mention their importance in economic and conservation management of specific organisms. However, the field of macroalgal genomics is hampered by difficulties in the isolation of suitable DNA. Even when DNA that appears high quality by standard metrics has been isolated, such samples may not perform well during the sequencing process. We here have compared Oxford Nanopore long-read sequencing results for three species of macroalgae to those of nonmacroalgal species and determined that when using macroalgal samples, sequencing activity declined rapidly, resulting in reduced sequencing yield. Chemical analysis of macroalgal DNA that would be considered suitable for sequencing revealed that DNA derived from dried macroalgae was enriched for polyphenol-DNA adducts (DNA with large polyphenols chemically attached to it), which may have led to sequencing inhibition. Of note, we observed the strongest evidence of sequencing inhibition and reduced sequence output when using samples dried using silica gel-suggesting that such storage approaches may not be appropriate for samples destined for Oxford Nanopore sequencing. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae and suggest a need to develop new storage methods that are more amenable to Oxford Nanopore sequencing or to use fresh flash-frozen tissue wherever possible for genome sequencing.