Biology subjects

Kamali, A.

Publications and source records attributed to Kamali, A..

6 recordsLinked to original sources

bioRxiv2025

Enhanced protein precipitation with ammonia enables rapid, universal extraction of oligonucleotides for bioanalysis

Extracting oligonucleotides from biological matrices for mass spectrometry (MS) using current methodologies is time-consuming and costly. Accelerating the discovery, characterization, and development of oligonucleotides (ONTs) requires a universal method that is low-cost, efficient, without requiring extensive method development for each new test article. Protein precipitation using organic solvents meets these criteria for small molecules but has historically failed for ONTs due to poor recovery arising from their tendency to co-precipitate with proteins. This study introduces an effective approach utilizing small amines dissolved in organic solvents to significantly boost extraction recovery of ONTs from biological matrices .We first present the methods development and then analytically qualify it for the bioanalysis of antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) extracted from various tissues, using ion-pairing reverse phase (IPRP) liquid chromatography coupled to tandem MS and high resolution MS (HRMS) detection. This method, Enhanced Protein Precipitation (EPP), achieves near-complete recovery across multiple ONT classes from biological matrices without need of sample digestion, costly solid phase extraction plates, or custom-designed hybridization probes. The method has proven to be more versatile and sustainable than conventional approaches. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/650521v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@a623d2org.highwire.dtl.DTLVardef@179b053org.highwire.dtl.DTLVardef@27273corg.highwire.dtl.DTLVardef@80fe47_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Host avoidance and resistance vary independently and are specific to parasite genotype

Hosts can reduce the negative fitness effects of parasite infection by avoiding contact with parasites or by resisting infection after contact. Because of their shared outcome, avoidance and resistance have been hypothesized to trade off with one another. Assuming these defenses carry fitness costs, hosts are expected to have high levels of one defense or the other, but not both. Alternatively, avoidance and resistance may covary positively, if, for example, they complement one another or are genetically or mechanistically linked. Testing these hypotheses requires measuring avoidance and resistance independently, which is challenging because they are functionally linked. In this study, we separated avoidance and resistance of the host C. elegans against the bacterial parasite S. marcescens and tested for a correlation between them. We phenotyped a panel of 12 genetically divergent hosts using two distinct bacterial strains and multiple experimental contexts. We found no evidence of a correlation between avoidance and resistance. This result suggests that avoidance and resistance can covary independently. Moreover, we found strong genetic specificity not only for resistance, but also for a measure of avoidance, motivating further research to examine the coevolutionary dynamics of avoidance.

evolutionary biology↗

bioRxiv2021

Evolution of protection after maternal immunization for respiratory syncytial virus in cotton rats

Maternal anti-respiratory syncytial virus (RSV) antibodies acquired by the fetus through the placenta protect neonates from RSV disease through the first weeks of life. In the cotton rat model of RSV infections, we previously reported that immunization of dams during pregnancy with virus-like particles assembled with mutation stabilized pre-fusion F protein as well as the wild type G protein resulted in robust protection of their offspring from RSV challenge (Blanco, et al Journal of Virology 93: e00914-19, https://doi.org/10.1128/JVI.00914-19). Here we describe the durability of those protective responses in dams, the durability of protection in offspring, and the transfer of that protection to offspring of two consecutive pregnancies without a second boost immunization. We report that four weeks after birth, offspring of the first pregnancy were significantly protected from RSV replication in both lungs and nasal tissues after RSV challenge, but protection was reduced in pups at 6 weeks after birth. However, the overall protection of offspring of the second pregnancy was considerably reduced, even at four weeks of age. This drop in protection occurred even though the levels of total anti-pre-F IgG and neutralizing antibody titers in dams remained at similar, high levels before and after the second pregnancy. The results are consistent with an evolution of antibody properties in dams to populations less efficiently transferred to offspring or the less efficient transfer of antibodies in elderly dams. Author SummaryRespiratory syncytial virus (RSV) is a major cause of acute lower respiratory tract infection of infants. Because there is no licensed vaccine for RSV as well as potential safety issues with any new vaccine, protection of infants from RSV is problematic. A possible safe approach for infant protection is the transfer of maternal anti-RSV antibodies, induced by immunization, across the placenta to the fetus serving to protect the newborn for months after birth. In a cotton rat model, we have previously shown that maternal immunization with virus-like particles assembled with the RSV F and G proteins protects offspring from RSV infection. Here we describe protection of offspring, following a single immunization, through two pregnancies showing that offspring of the first were well protected from RSV challenge. However, offspring of the second pregnancy were very weakly protected although the levels of total anti-pre-F antibodies and neutralizing antibody titers in the dams remained at constant and high levels before and after the second pregnancy. This result is consistent with an evolution of antibody properties in the dams to those less efficiently transferred to offspring and highlights the importance of appropriate strategies for maternal immunization, such as immunization during each pregnancy.

microbiology↗

bioRxiv2020

Human Adenovirus Type 4 Comprises Two Mayor Phylogroups With Distinct Phenotypes Relevant To Pathogenesis

Human adenovirus type 4 (HAdV-E4) is the only type (and serotype) classified within species Human mastadenovirus E that has been isolated from a human host to the present. Recent phylogenetic analysis of whole genome sequences of strains representing the spectrum of intratypic genetic diversity described to date identified two major evolutionary lineages designated phylogroups (PG) I, and II, and validated the early clustering of HAdV-E4 genomic variants into two major groups by low resolution restriction fragment length polymorphism analysis. In this study we expanded our original analysis of intra- and inter-PG genetic variability, and used a panel of viruses representative of the spectrum of genetic diversity described for HAdV-E4 to examine the magnitude of inter- and intra-PG phenotypic diversity using an array of cell-based assays and a cotton rat model of HAdV respiratory infection. Our proteotyping of HAdV-E strains using concatenated protein sequences in selected coding regions including E1A, E1B-19K and -55K, DNA polymerase, L4-100K, various E3 proteins, and E4-34K confirmed that the two clades encode distinct variants/proteotypes at most of these loci. Our in vitro and in vivo studies demonstrated that PG I and PG II differ in their growth, spread, and cell killing phenotypes in cell culture and in their pulmonary pathogenic phenotypes. Surprisingly, the differences in replicative fitness documented in vitro between PGs did not correlate with the differences in virulence observed in the cotton rat model. This body of work is the first reporting phenotypic correlates of naturally occurring intratypic genetic variability for HAdV-E4. IMPORTANCEHuman adenovirus type 4 (HAdV-E4) is a prevalent causative agent of acute respiratory illness of variable severity and of conjunctivitis and comprises two major phylogroups that carry distinct coding variations in proteins involved in viral replication and modulation of host responses to infection. Our data show that PG I and PG II are intrinsically different regarding their ability to grow and spread in culture and to cause pulmonary disease in cotton rats. This is the first report of phenotypic divergence among naturally occurring known genetic variants of a HAdV type of medical importance. This research reveals readily detectable phenotypic differences between strains representing phylogroups I and II, and it introduces a unique experimental system for the elucidation of the genetic basis of adenovirus fitness and virulence and thus for increasing our understanding of the implications of intratypic genetic diversity in the presentation and course of HAdV-E4-associated disease.

microbiology↗

bioRxiv2019

The transferability of lipid-associated loci across African, Asian and European cohorts

The under-representation of non-European samples in genome-wide association studies could ultimately restrict who benefits from medical advances through genomic science. Our aim was therefore to address the fundamental question whether causal variants for blood lipids are shared across populations.\n\nA polygenic score based on established LDL-cholesterol-associated loci from European discovery samples had consistent effects on serum levels in samples from the UK, Uganda and Greek population isolates (correlation coefficient r=0.23 to 0.28 per LDL standard deviation, p<1.9x10-14). Trans-ethnic genetic correlations between European ancestry, Chinese and Japanese cohorts did not differ significantly from 1 for HDL, LDL and triglycerides. In each study, >60% of major lipid loci displayed evidence of replication with one exception. There was evidence for an effect on serum levels in the Ugandan samples for only 10% of major triglyceride loci. The PRS was only weakly associated in this group (r=0.06, SE=0.013). We establish trans-ethnic colocalization as a method to distinguish shared from population-specific trait loci.\n\nOur results provide evidence for high levels of consistency of genetic associations for cholesterol biomarkers across populations. However, we also demonstrate that the degree of shared causal genetic architecture can be population-, trait- and locus-specific. Efforts to implement genetic risk prediction in clinical settings should account for this.

genetics↗

bioRxiv2018

Retention of adults from fishing communities in an HIV vaccine preparedness study in Masaka, Uganda

IntroductionPeople living in fishing communities around Lake Victoria may be suitable for enrolment in HIV prevention trials because of high HIV incidence. We assessed the ability to recruit and retain individuals from fishing communities into an HIV vaccine preparedness cohort study in Masaka, Uganda.\n\nMethodsHIV high risk, sero-negative adults (18-49 years) were identified from four fishing villages bordering Lake Victoria through door-to-door HIV counselling and testing (HCT). Interested persons were referred for: screening, enrolment, and quarterly follow-up visits at a study clinic located approximately 40 kilometres away. Repeat HCT, HIV risk assessment, and evaluation and treatment for sexually transmitted infections were provided. Rates of and factors associated with study dropout were assessed using Poisson regression models.\n\nResultsA total of 940 participants were screened between January 2012 and February 2015, of whom 654 were considered for the analysis. Over a two-year follow-up period, 197 (30.1%) participants dropped out of the study over 778.9 person-years, a dropout rate of 25.3 / 100 person-years. Dropout was associated with being female (aRR =1.56, 95% confidence interval [CI] 1.12-2.18), age, being 18-24 years (aRR=1.64; 95% CI 1.03-2.60), 25-34 years (aRR=1.63; 95% CI 1.04-2.55); having no education (aRR=2.02; 95% CI: 1.23-3.31); living in the community for less than one year (aRR=2.22; 95% CI: 1.46-3.38) or 1-5 years (aRR=1.68; 95% CI: 1.16-2.45) and occupation.\n\nConclusionsIt is possible to recruit and retain individuals from fishing communities, however, intensified participant tracing may be necessary in a vaccine trial to keep in follow up female, young, less educated, those in mobile occupations and new residents.

epidemiology↗