Explore the vast range of titles available.

Dengue is the most rapidly expanding arboviral disease in India. Aedes aegypti is the primary vector of dengue fever. Chemical insecticides have long been used in the vector control programmes along with other control measures. However, continuous use of insecticides targeting Ae. aegypti may lead to development of insecticide resistance. Though resistance in Ae. aegypti has been reported, the mutation in ace-1 gene associated with temephos resistance is not reported in natural populations. The present study aims to evaluate the susceptibility/resistance status of Ae. aegypti to temephos from three districts of Tamil Nadu. Ae. aegypti larvae were sampled from different locations in three districts, viz., Dharmapuri, Salem and Namakkal. The standard WHO larval bioassay, biochemical assays and spotting of specific mutation (G119S) in the acetylcholinesterase gene, which is associated with organophosphate resistance, were carried out by PCR and sequencing. The results showed that larvae from Namakkal (NKL) population had an alteration in their susceptibility status (RR = 6.9 fold), while the other populations were moderately susceptible to insecticides. Biochemical assay showed increased activity for α- and β-esterase in NKL, as well as evidence of acetylcholinesterase insensitivity. G119S mutation was detected in this population with high frequency of 0.24. The high activity of esterase, mixed-function oxidase (MFO) and ace-1 mutation frequency were closely associated with temephos resistance. Early detection of resistance alleles in natural vector population could be useful for the successful implementation of insecticide resistance management strategies. The results of this study provide baseline data on temephos resistance in Ae. aegypti populations.

Epidemiological studies revealed an increased risk for kidney cancer in hypertensive patients. In many of these patients, the blood pressure regulating renin–angiotensin–aldosterone system (RAAS) is activated. A stimulated RAAS leads to oxidative stress and increases markers of DNA damage, both in vitro and in animal models of hypertension. However, the mutagenic potential of RAAS activation has not been investigated yet. To quantify hypertension-induced mutations, BigBlue®+/− rats, which carry a transgenic lacI gene for mutation analysis, were treated for 20 weeks with a mean dose of 400 µg angiotensin II/kg × day. Angiotensin II-treated animals showed significantly increased blood pressure and impaired kidney function. Urinary excretion of oxidized nucleobases was raised. Additionally, in the renal cortex, oxidative stress, oxidatively generated DNA lesions and DNA strandbreaks were significantly increased. Further, a significant elevation of the mutant frequency in kidney DNA was detected. Sequencing revealed the presence of GC → T:A transversions in the mutated lacI genes of the angiotensin II-treated animals as a result of unrepaired oxidatively modified DNA bases, while no such transversions were found in the mutated lacI genes from control animals. The results demonstrate that the oxidative stress and DNA damage previously observed in kidney cells in vitro and in vivo after angiotensin II treatment indeed is associated with the accumulation of mutations in rat kidneys, providing further evidence for a cancer-initiating potential of elevated angiotensin II concentrations.

A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors). This pathway-centric method shows high sensitivity compared with gene-centric analyses of mutation data. Notably, only a marginal decrease in performance is observed when using 10 % of TCGA patient samples, suggesting the method may potentiate cancer genome projects with small patient populations.

Low-frequency HIV variants possessing resistance mutations against non‑nucleoside reverse transcriptase inhibitors (NNRTI), especially at HIV reverse transcriptase (RT) amino acid (aa) positions K103 and Y181, have been shown to adversely affect treatment response. Therapeutic failure correlates with both the mutant viral variant frequency and the mutational load. We determined the prevalence of NNRTI resistance mutations at several RT aa positions in viruses from 204 antiretroviral (ARV)-naïve HIV-infected individuals using deep sequencing, and examined the relationship between mutant variant frequency and mutational load for those variants. Deep sequencing to ≥0.4% levels found variants with major NNRTI-resistance mutations having a Stanford-HIVdb algorithm value ≥30 for efavirenz and/or nevirapine in 52/204 (25.5%) ARV-naïve HIV-infected persons. Eighteen different major NNRTI mutations were identified at 11 different positions, with the majority of variants being at frequency >1%. The frequency of these variants correlated strongly with the mutational load, but this correlation weakened at low frequencies. Deep sequencing detected additional major NNRTI-resistant viral variants in treatment-naïve HIV-infected individuals. Our study suggests the significance of screening for mutations at all RT aa positions (in addition to K103 and Y181) to estimate the true burden of pre-treatment NNRTI-resistance. An important finding was that variants at low frequency had a wide range of mutational loads (>100-fold) suggesting that frequency alone may underestimate the impact of specific NNRTI-resistant variants. We recommend further evaluation of all low-frequency NNRTI-drug resistant variants with special attention given to the impact of mutational loads of these variants on treatment outcomes.

The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth response of Escherichia coli to sub-inhibitory and inhibitory concentrations of nine antibiotics. We found that the heterogeneity in growth increases more than what is expected from growth rate reduction for three out of the nine antibiotics tested. For two antibiotics (rifampicin and nitrofurantoin), we found that sub-populations were able to maintain growth at lethal antibiotic concentrations for up to 10 generations. This perseverance of growth increased the population size and led to an up to 40-fold increase in the frequency of antibiotic resistance mutations in gram-negative and gram-positive species. We conclude that antibiotic perseverance is a common phenomenon that has the potential to impact antibiotic resistance development across pathogenic bacteria.

Cancer genomics aims to personalize treatments by identifying genetic abnormalities in cancer cells. However, current analytical techniques face limitations in simplicity and cost-effectiveness. To address these issues, we developed an enhanced capillary gel electrophoresis (CE) sequencer using a fluorescence-acquisition technique called “HiDy” (High Dynamic range) (HiDy-CE). The HiDy-CE reduces the hardware binning region size and increases the number of regions on a charge-coupled device image sensor, expanding the dynamic range and reducing saturation risk. By applying the multi-base primer extension method to the HiDy-CE with control DNA containing known mutations, we detected variant allele frequencies (VAFs) as low as 0.5% for major KRAS hotspot mutation at codon 12 and 13. With 10 ng of DNA from small tissues obtained via fine-needle biopsy from patients with suspected pancreaticoduodenal tumors, HiDy-CE produced equivalent VAFs in KRAS compared with targeted amplicon sequencing. This demonstrated the world’s first capability of detecting mutations below 1% on CE using pathological specimens, leveraging its wide dynamic range. With only 2 ng of input DNA, the HiDy-CE provided results highly concordant with digital PCR with minimal non-specific noise. These findings underscore the HiDy-CE’s potential for sensitive detection of oncogenes such as KRAS , facilitating pre-testing before comprehensive genome profiling.

The fall armyworm (FAW), Spodoptera frugiperda invaded China in December 2018 and has since spread quickly countrywide. Two sympatric biotype strains of FAW, rice-strain and corn-strain, have been classified and showed to have different susceptibilities to chemical insecticides. Present FAW control has primarily relied on insecticides, which resulted in a rapid evolution of the resistance to insecticides in FAW. Herein, sixteen geographical populations of FAW were collected annually from maize fields in China between 2019 and 2021, both Tpi genotyping ( n  = 3079) and feeding preference bioassay ( n  = 2892) showed Chinese FAW were predominantly the corn-strain. Resistance monitoring revealed that FAW had not evolved resistance to chlorantraniliprole since it invaded China with RRs of 0.32–2.32 and a very low mutation frequency RyR of 0.14%. Most FAW populations were susceptible to emamectin benzoate, spinetoram, indoxacarb, lambda-cyhalothrin and acephate. However, low resistance levels (5 < RR < 10) were detected in some populations, suggesting rotational or mixed applications of insecticides and further resistance monitoring must be strengthened to prevent or delay the development of insecticide resistance. The mutation frequency of ace-1 at the locus A201S and F290V was 21.27% and 84.51%, respectively. The mutation frequency of VGSC at the locus T929I and L1014F was 0.11% and 0.15%, respectively. The detoxification enzyme activities of P450s, ESTs and GSTs were relatively consistent among different populations. Our study provides a systematical understanding of the current genetic architecture and resistance status of FAW in China and will contribute to the region-wide chemical control and the development of resistance management strategies for FAW in China.

Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs; we report the GSSPs constructed for 69 common human V genes (DOI: 10.6084/m9.figshare.3511083) and provide high-resolution logo plots for each (DOI: 10.6084/m9.figshare.3511085).

De novo mutations (DNMs) are drivers of genetic disorders. However, the study of DNMs is hampered by technological limitations preventing accurate quantification of ultra-rare mutations. Duplex Sequencing (DS) theoretically has < 1 error/billion base-pairs (bp). To determine the DS utility to quantify and characterize DNMs, we analyzed DNA from blood and spermatozoa from six healthy, 18-year-old Swedish men using the TwinStrand DS mutagenesis panel (48 kb spanning 20 genic and intergenic loci). The mean single nucleotide variant mutation frequency (MF) was 1.2 × 10 − 7 per bp in blood and 2.5 × 10 − 8 per bp in sperm, with the most common base substitution being C > T. Blood MF and substitution spectrum were similar to those reported in blood cells with an orthogonal method. The sperm MF was in the same order of magnitude and had a strikingly similar spectrum to DNMs from publicly available whole genome sequencing data from human pedigrees (1.2 × 10 − 8 per bp). DS revealed much larger numbers of insertions and deletions in sperm over blood, driven by an abundance of putative extra-chromosomal circular DNAs. The study indicates the strong potential of DS to characterize human DNMs to inform factors that contribute to disease susceptibility and heritable genetic risks.

Cancer cells contain numerous clonal mutations, i.e., mutations that are present in most or all malignant cells of a tumor and have presumably been selected because they confer a proliferative advantage. An important question is whether cancer cells also contain a large number of random mutations, i.e., randomly distributed unselected mutations that occur in only one or a few cells of a tumor. Such random mutations could contribute to the morphologic and functional heterogeneity of cancers and include mutations that confer resistance to therapy. We have postulated that malignant cells exhibit a mutator phenotype resulting in the generation of random mutations throughout the genome. We have recently developed an assay to quantify random mutations in human tissue with unprecedented sensitivity. Here, we report measurements of random single-nucleotide substitutions in normal and neoplastic human tissues. In normal tissues, the frequency of spontaneous random mutations is exceedingly low, less than 1 x 10⠻⠸ per base pair. In contrast, tumors from the same individuals exhibited an average frequency of 210 x 10⠻⠸ per base pair, an elevation of at least two orders of magnitude. Our data document tumor heterogeneity at the single-nucleotide level, indicate that accelerated mutagenesis prevails late into tumor progression, and suggest that elevation of random mutation frequency in tumors might serve as a novel prognostic indicator.