Biology subjects

Tamim, S.

Publications and source records attributed to Tamim, S..

6 recordsLinked to original sources

bioRxiv2026

Phylodynamic Analysis of the Global Dispersal and Spatiotemporal Dynamics of HIV-1 Subtype C

HIV-1 subtype C is the most prevalent HIV clade globally, yet its cross-continental transmission dynamics remain incompletely resolved due to sampling biases and unquantified analytical uncertainty. We performed a large-scale phylodynamic analysis of 1,221 near full-length genomic sequences from 32 countries (1986-2019). Employing a stratified subsampling strategy to mitigate bias, we systematically benchmarked 16 method combinations, pairing four maximum likelihood phylogenetic tools (FastTree, IQ-TREE, PhyML, RAxML-NG) with four temporal dating methods (TempEst, LSD, treedater, TreeTime). Topological analysis revealed significant discordance between rapid heuristics and higher-precision estimators. The estimated time to the most recent common ancestor (TMRCA) and the timing of individual introductions were highly sensitive to the temporal dating method, while evolutionary rates varied across both phylogenetic and temporal tools. Crucially, counts of viral introductions and the reconstruction of spatial transmission networks were statistically robust across all 16 combinations. Phylogeographic reconstruction confirmed a dominant, recurring dispersal corridor from Africa to Europe, with independent secondary reservoirs in South America and Asia. Ancestral trait reconstruction demonstrated transmission is primarily driven by heterosexual networks, within which "Not Recorded" risk groups were phylogenetically nested. This multi-method benchmarking reveals that while exact chronologies are sensitive to methodological choices, spatial network reconstructions and source-sink classifications remain remarkably consistent. These findings provide a robust map of subtype Cs global expansion and establish highly reliable, scalable workflows for resolving spatial dissemination routes for real-time genomic epidemiology.

evolutionary biology↗

bioRxiv2025

Integrating phylodynamics and historical records reveals decades-old introductions of PRRSV into Costa Rica via international swine trade

BackgroundIn August 1995, necropsies on post-weaning piglets from the CA-CART farm in the province of Cartago, Costa Rica, revealed respiratory lesions, pleuritis, peritonitis, and arthritis. Skin lesions were also observed, progressing to scabs. A subsequent outbreak in 1996 prompted antibiotic administration. Mortality analysis from 1990 to 1995 showed no significant seasonal patterns, but yearly variations were noted. Piglets born in Costa Rica from imported gilts had a higher average mortality rate (10.65%) than the 8.11% mortality rate for piglets born from non-imported gilts and sows or imported sows (p = 0.002). MethodsIn March 1996, serum samples were sent for potential PRRS virus (PRRSV) diagnosis, and 10 PRRSV-2 ORF5 sequences collected during a prospective study from 2019-2021 were obtained from various locations in the country. In this article, we seek to investigate the evolutionary and spatio-temporal dynamics of PRRSV-2 in Costa Rica in the context of international swine movements using the phylodynamic framework integrated with the BEAST package. Results and DiscussionThe phylodynamic modeling estimated at least two independent PRRSV-2 introductions into the country. The earliest introduction occurred around 1978 (95% highest posterior density interval: 1959.01-1997.54) and led to the viruses circulating in the farm 1CRC with an origin from Japan, possibly via US swine exports. A second cluster, 4CRC, subsequently emerged within Costa Rica from the earlier 1CRC lineage (1990.24; 95% HPD interval = 1976.15-2010.30). Another viral introduction from the US occurred around 1991 (95% highest posterior density interval: 1974.34-2011.35) and established the 3CRC cluster. Though the viral introduction was traced back to the US, the limited genomic surveillance of PRRSV leaves room for considering alternative origins. ConclusionOur findings provide a high-resolution model of how international swine trade drives the introduction and evolution of a major livestock pathogen, highlighting the critical need for integrating genomic surveillance into biosecurity protocols.

microbiology↗

bioRxiv2020

A transposon surveillance mechanism that safeguards plant male fertility during stress

Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how MAGO2 activity and its interaction with retrotransposon RNA targets are modulated through the dynamic phosphorylation of a set of highly conserved surface-located serine residues. Our results demonstrate that an Argonaute-dependent RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions by controlling the mutagenic activity of transposons in male germ cells.

plant biology↗

bioRxiv2020

Ligation bias is a major contributor to nonstoichiometric abundances of secondary siRNAs and impacts analyses of microRNAs

Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. High-throughput sequencing is used for the discovery and quantification of small RNAs. However, several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two stages of maize anthers to evaluate the performance of seven commercially-available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phasiRNAs, or tRNA-derived fragment. We also observed that ligation bias occurs at both ends of miRNAs and phasiRNAs, suggesting that the biased compositions observed in small RNA populations, including nonstoichiometric levels of phasiRNAs within a locus, may reflect a combination of biological and technical influences.

plant biology↗

bioRxiv2020

Environment-conditioned male fertility of HD-ZIP IV transcription factor mutant ocl4: impact on 21-nt phasiRNA accumulation in pre-meiotic maize anthers

Environment-conditioned genic male sterility is a key strategy used to produce hybrid seeds efficiently in many crops, with the exception of maize. The underlying molecular mechanisms of environment-conditioned sterility are poorly understood. Here, we report a derivative line of the male sterile outer cell layer 4 (ocl4) mutant of maize, in which fertility was restored and perpetuated over several generations, under warm growing conditions. Conditionally fertile ocl4 anthers exhibit the anatomical abnormality of a partially duplicated endothecial layer, just like their sterile counterparts. We profiled the dynamics of phased, small interfering RNAs (phasiRNAs) during pre-meiotic development in fully sterile and various grades of semi-fertile ocl4 anthers. We found that the biogenesis of 21-nt phasiRNAs is largely dependent on Ocl4 at three key steps: (1) production of PHAS precursor transcripts, (2) expression of miR2118 that modulates precursor processing, and (3) accumulation of 21-nt phasiRNAs. We propose that 21-nt reproductive phasiRNAs buffer development under unfavorable environmental conditions and are dispensable under favorable conditions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2018

The basis of accumulation differences in plant 21-nt reproductive phasiRNAs, and their cis-directed activity

O_LIPost-transcriptional gene silencing in plants results from independent activities of diverse small RNA types. In anthers of grasses, hundreds of loci yield non-coding RNAs that are processed into 21- and 24-nt phased small interfering RNAs (phasiRNAs); these are triggered by miR2118 and miR2275.\nC_LIO_LIWe characterized these \"reproductive phasiRNAs\" from rice panicles and anthers across seven developmental stages. Our computational analysis identified characteristics of the 21-nt reproductive phasiRNAs that impact their biogenesis, stability, and potential functions.\nC_LIO_LIWe demonstrate that 21-nt reproductive phasiRNAs can function in cis to target their own precursors. We observed evidence of this cis regulatory activity in both rice (Oryza sativa) and maize (Zea mays). We validated this activity with evidence of cleavage and a resulting shift in the pattern of phasiRNA production.\nC_LIO_LIWe characterize biases in phasiRNA biogenesis, demonstrating that the Pol II-derived \"top\" strand phasiRNAs are consistently higher abundance than the bottom strand. The first phasiRNA from each precursor overlaps the miR2118 target site, and this impacts phasiRNA accumulation or stability, evident in the weak accumulation of this phasiRNA position. Additional influences on this first phasiRNA duplex include the sequence composition and length, and we show that these factors impact Argonaute loading.\nC_LI

plant biology↗