Biology subjects

Zhang, S.-M.

Publications and source records attributed to Zhang, S.-M..

4 recordsLinked to original sources

bioRxiv2026

NPlasmid-seq: Cas9-encoded terminal signatures enable molecule-level nanopore quality control of vector and IVT-template plasmids

Consensus-based plasmid quality control can overlook structural heterogeneity within a preparation. We developed NPlasmid-seq, a Cas9-guided nanopore workflow that encodes sample identity through paired terminal signatures generated at predefined backbone positions, without sample-specific oligonucleotide barcodes. We cleavage-validated 24 sgRNAs. In five representative assigned read bins, each bin showed its strongest sequence agreement with its cognate reference. Contaminant detection was evaluated with a single class-specific classifier applied both to computational read mixtures and to physical DNA mixtures, placing the two designs on a common scale. In computational read mixtures of 5,000 reads, a contaminant was detected in all 20 independent subsamples at each of 0.2%, 0.5%, 1% and 5% abundance and in 13 of 20 subsamples at 0.1%; precision was 1.000 in all 100 subsamples, with no false-positive calls among 493,200 reads from the declared target plasmid. In physical DNA mixtures carried through cleavage, pooled library preparation and sequencing, a contaminant was detected in all six samples prepared at 0.5 mol% input and all six at 1 mol%. Observed read fractions did not distinguish the 0.5 and 1 mol% input levels. Instead, they differed systematically by 4.0-fold between preparation pools, a larger effect than the difference between the two input levels. We therefore interpret the workflow as a detector, not a quantifier, of sub-percent contamination. Read-level analysis identified a recurrent 93-bp deletion in 61.7% of reads from a preparation that had passed consensus-based quality control. Sanger genotyping of 24 colonies identified deletion-type profiles in 10 colonies and intact-type profiles in three. The remaining 11 colonies showed double peaks at the diagnostic locus, consistent with coexistence of both sequence forms within individual clones. In in vitro transcription template plasmids, longer poly(A) tracts were associated with higher multimeric-read fractions. Across ten matched A90 culture pairs, propagation at 30 degree reduced these fractions relative to 37 degree (paired t-test, P = 0.0098). These measurements describe recovered read populations, not absolute molecular abundances. NPlasmid-seq therefore complements consensus validation by revealing sequence and structural heterogeneity within a preparation and by identifying a culture condition associated with a lower multimeric-read fraction.

bioengineering↗

bioRxiv2020

Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-{beta} signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

genetics↗

bioRxiv2018

The in vivo transcriptome of Schistosoma mansoni in two prominent vector species, Biomphalaria pfeifferi and B. glabrata

BackgroundThe full scope of the genes expressed by schistosomes during intramolluscan development has yet to be characterized. Understanding the gene products deployed by larval schistosomes in their snail hosts will provide insights into their establishment, maintenance, asexual reproduction, ability to castrate their hosts, and their prolific production of human-infective cercariae. Using the Illumina platform, the intramolluscan transcriptome of Schistosoma mansoni was investigated in field-derived specimens of the prominent vector species Biomphalaria pfeifferi at 1 and 3 days post infection (d) and from snails shedding cercariae. These S. mansoni samples were derived from the same snails used in our complementary B. pfeifferi transcriptomic study. We supplemented this view with microarray analyses of S. mansoni from B. glabrata at 2d, 4d, 8d, 16d, and 32d.\n\nPrincipal FindingsTranscripts representing at least 7,740 (66%) of known S. mansoni genes were expressed during intramolluscan development, with the greatest number expressed in snails shedding cercariae. Many transcripts were constitutively expressed throughout development featuring membrane transporters, and metabolic enzymes involved in protein and nucleic acid synthesis and cell division. Several proteases and protease inhibitors were expressed at all stages, including some proteases usually associated with cercariae. Transcripts associated with G-protein coupled receptors, germ cell perpetuation, and stress responses and defense were well represented. We noted transcripts homologous to planarian anti-bacterial factors, several neural development or neuropeptide transcripts including neuropeptide Y, and receptors that may be associated with schistosome germinal cell maintenance and that could also impact host reproduction. In at least one snail the presence of larvae of another digenean species (an amphistome) was associated with repressed S. mansoni transcriptional activity.\n\nConclusions/SignificanceThis in vivo study, particularly featuring field-derived snails and schistosomes, provides a distinct view from previous studies of development of cultured intramolluscan stages from lab-maintained organisms. We found many highly represented transcripts with suspected or unknown functions, with connection to intramolluscan development yet to be elucidated.\n\nAUTHOR SUMMARYSchistosoma mansoni is one of the most important schistosome species causing the neglected tropical disease human intestinal schistosomiasis. By focusing on S. mansoni in vivo with its broadly distributed sub-Saharan African snail intermediate host, Biomphalaria pfeifferi, we uncover new insights and basic knowledge of this host-parasite relationship that are critical for understanding schistosomiasis transmission. We show that in vivo studies, particularly using field-derived specimens, provides a distinct view from the uniformed transcriptional responses traditionally seen from in vitro studies on S. mansoni and Biomphalaria snails. With the growing consensus that we need to supplement chemotherapy with other control methods, understanding how S. mansoni interacts with its obligatory snail host becomes integral for future planning of control programs. The data provided within provides specific analysis on how the schistosomes successfully protect themselves from host defenses and the necessary transcriptional responses required for its amplifying asexual proliferation that result in human-infective cercariae.

molecular biology↗

bioRxiv2018

Transcriptional responses of Biomphalaria pfeifferi and Schistosoma mansoni following exposure to niclosamide, with evidence for a synergistic effect on snails following exposure to both stressors

BackgroundSchistosomiasis is one of the worlds most common NTDs. Successful control operations often target snail vectors with the molluscicide niclosamide. Little is known about how niclosamide affects snails, including for Biomphalaria pfeifferi, the most important vector for Schistosoma mansoni in Africa. We used Illumina technology to explore how field-derived B. pfeifferi, either uninfected or harboring cercariae-producing S. mansoni sporocysts, respond to a sublethal exposure of niclosamide. This study afforded the opportunity to determine if snails respond differently to biotic or abiotic stressors, and if they reserve unique responses for when presented with both stressors in combination. We also examined how sporocysts respond when their snail host is exposed to niclosamide.\n\nPrincipal FindingsCercariae-producing sporocysts within snails exposed to niclosamide express ~68% of the genes in the S. mansoni genome, as compared to 66% expressed by intramolluscan stages of S. mansoni in snails not exposed to niclosamide. Niclosamide does not disable sporocysts nor does it seem to provoke from them distinctive responses associated with detoxifying a xenobiotic. For B. pfeifferi, niclosamide treatment alone increases expression of several features not up-regulated in infected snails including particular cytochrome p450s and heat shock proteins, glutathione-S-transferases, antimicrobial factors like LBP/BPI and protease inhibitors, and also provokes strong down regulation of proteases. Exposure of infected snails to niclosamide resulted in numerous up-regulated responses associated with apoptosis along with down-regulated ribosomal and defense functions, indicative of a distinctive, compromised state not achieved with either stimulus alone.\n\nConclusions/SignificanceThis study helps define the transcriptomic responses of an important and under-studied schistosome vector to S. mansoni sporocysts, to niclosamide, and to both in combination. It suggests the response of S. mansoni sporocysts to niclosamide is minimal and not reflective of a distinct repertoire of genes to handle xenobiotics while in the snail host. It also offers new insights for how niclosamide affects snails.\n\nAuthorS SummarySchistosomaisis control programs often employ the use of chemical molluscicides, such as niclosamide, to control the obligatory intermediate snail hosts. Despite its widespread use, we know little about how niclosamide affects snails like Biomphalaria pfeifferi, the most important vector Schistosoma mansoni in Africa. By sequencing the transcriptomes of uninfected and S. mansoni-infected B. pfeifferi exposed to niclosamide, we analyze the snails response to both biotic and abiotic stressors. We can also examine the response of S. mansoni to niclosamide exposure during intramolluscan development. Biomphalaria pfeifferi snails exposed only to niclosamide showed unique up-regulation of stress and defense-related transcripts not seen in snails infected with a biotic, like S. mansoni infection, alone. Schistosoma mansoni-infected B. pfeifferi exposed to niclosamide were clearly unable to regulate normal metabolic and detoxification processes. Cercariae-producing sporocysts within snails exposed to niclosamide are largely unaffected and continue to produce transcripts required for cercariae production.

molecular biology↗