Biology subjects

Siddiqui, S.

Publications and source records attributed to Siddiqui, S..

23 records · Page 2Linked to original sources

bioRxiv2019

Factors Affecting Detection Of GMO Traces In Food And Crop Samples

Rice is one of the highly consumable and demanded food crops throughout the world. To meet this requirement, genetically modified (GM) crops were introduced, which were met with sturdy and frequently angry opposition by the user. To handle the situation labeling of GM food / crop was advised, thus demand for traceability and detection of unknown modified genes increased. Modified genes are detected by various methods; these methods are affected by several factors as reported in international standards. Those factors include presence / absence of shells, husk, and dust, method of DNA extraction and different PCR primers. These factors ultimately pose hindrance in detection of modified genes. This study was conducted to analyze the effects of the above mentioned factors on detection of GM rice samples. Furthermore two different sets of primers were used with same samples and their impact on the PCR detection was observed. The results showed a significant difference in DNA concentration between the rice samples with husk, without husk and after seed germination. Furthermore, the change of PCR primer set also affected the detection of genetic modifications. This allows analysis of the potential factors that may have impact on the final results.

plant biology↗

bioRxiv2019

Efficient RNP-directed human gene targeting reveals SPDEF is required for IL-13-induced mucostasis

Primary human bronchial epithelial cell (HBEC) cultures are a useful model for studies of lung health and major airway diseases. However, mechanistic studies have been limited by our ability to selectively disrupt specific genes in these cells. Here we optimize methods for gene targeting in HBECs by direct delivery of single guide RNA (sgRNA) and recombinant Cas9 (rCas9) complexes by electroporation, without a requirement for plasmids, viruses, or antibiotic selection. Variations in the method of delivery, sgRNA and rCas9 concentrations, and sgRNA sequences all had effects on targeting efficiency, allowing for predictable control of the extent of gene targeting and for near complete disruption of gene expression. To demonstrate the value of this system, we targeted SPDEF, which encodes a transcription factor previously shown to be essential for the differentiation of MUC5AC-producing goblet cells in mouse models of asthma. Targeting SPDEF led to proportional decreases in MUC5AC expression in HBECs stimulated with IL-13, a central mediator of allergic asthma. Near-complete targeting of SPDEF abolished IL-13-induced MUC5AC expression and goblet cell differentiation. In addition, targeting of SPDEF prevented IL-13-induced impairment of mucociliary clearance, which is likely to be an important contributor to airway obstruction, morbidity, and mortality in asthma. We conclude that direct delivery of sgRNA and rCas9 complexes allows for predictable and efficient gene targeting and enables mechanistic studies of disease-relevant pathways in primary HBECs.

molecular biology↗

bioRxiv2018

Modeling the relative role of human mobility, land-use and climate factors on dengue outbreak emergence in Sri Lanka

BackgroundMore than 80,000 dengue cases including 215 deaths were reported nationally in less than seven months between 2016-2017, a fourfold increase in the number of reported cases compared to the average number over 2010-2016. The region of Negombo, located in the Western province, experienced the greatest number of dengue cases in the country and is the focus area of our study, where we aim to capture the spatial-temporal dynamics of dengue transmission.\n\nMethodsWe present a statistical modeling framework to evaluate the spatial-temporal dynamics of the 2016-2017 dengue outbreak in the Negombo region of Sri Lanka as a function of human mobility, land-use, and climate patterns. The analysis was conducted at a 1 km x 1 km spatial resolution and a weekly temporal resolution.\n\nResultsOur results indicate human mobility to be a stronger indicator for local outbreak clusters than land-use or climate variables. The minimum daily temperature was identified as the most influential climate variable on dengue cases in the region; while among the set of land-use patterns considered, urban areas were found to be most prone to dengue outbreak, followed by areas with stagnant water and then coastal areas. The results are shown to be robust across spatial resolutions.\n\nConclusionsOur study highlights the potential value of using travel data to target vector control within a region. In addition to illustrating the relative relationship between various potential risk factors for dengue outbreaks, the results of our study can be used to inform where and when new cases of dengue are likely to occur within a region, and thus help more effectively and innovatively, plan for disease surveillance and vector control.

epidemiology↗

bioRxiv2018

Policy lessons from spatiotemporal enrollment patterns of Payment for Ecosystem Service Programs in Argentina

Over the last 50 years, payment for ecosystem services schemes (PES) have been lauded as a market-based solution to curtail deforestation and restore degraded ecosystems. However, PES programs often fail to conserve sites under strong long-term deforestation pressures and allocate financial resources without having a sizeable impact on long-term land use change. Underperformance, in part, is likely due to adverse selection as landowners with land at the lowest threat from conversion or loss may be most likely to enroll or enrollment may be for short time-periods. Improving program performance to overcome adverse selection requires understanding attributes of landowners and their land across large scales to identify spatial and temporal enrollment patterns that drive adverse selection. In this paper, we examine these patterns in Argentinas PES program in the endangered Chaco forest ecoregion, which was established in 2007 under the National Forest Law. Our study area covers 252,319 km2. Among our most important findings is that large parcels of enrolled land and land owned by absentee landowners show greater evidence of spatiotemporal adverse selection than smaller plots of land and land owned by local actors. Furthermore, lands managed for conservation and restoration are more likely to be associated with adverse selection than lands that provide financial returns such as harvest of non-timber forest products, silviculture, and silvopasture. However, prior to recommending that PES programs focus on land uses with higher potential earnings, a greater understanding is needed of the degree to which these land uses meet ecological and biodiversity goals of PES programs. Because of this, we posit that a PES incorporating a market-based compensation strategy that varies with commodity prices, along with approaches that provide incentives for conservation and restoration land uses and enrollment of local landowners, could promote long-term conservation of endangered lands.

ecology↗

bioRxiv2018

Structural variation detection by proximity ligation from FFPE tumor tissue

The clinical management and therapy of many solid tumor malignancies is dependent on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call \"Fix-C\", which is similar in concept to Hi-C. Fix-C enables structural variation detection from fresh and archival FFPE samples. We applied this method to 15 clinical adenocarcinoma and sarcoma specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with FISH assays - the current clinical gold standard. Additionally, we are able to identify novel structural variation undetected by other methods and recover long-range chromatin configuration information from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material, and inform the development of targeted molecular diagnostic assays for patient care.

genomics↗