Biology subjects

Unlu, I.

Publications and source records attributed to Unlu, I..

5 recordsLinked to original sources

bioRxiv2026

RecBCD Prevents Bacterial Autoimmunity by Clearing Self-DNA Ends Produced During Replication Termination

Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to trigger the P2-encoded OLD antiphage system. Normally, these physiological triggers are cleared by the dual helicase-nuclease activities of the conserved RecBCD enzyme, which acts as an immune safeguard analogous to mammalian TREX1 exonuclease and plant DBR1 debranching enzyme. However, when this clearance fails, the transient self-DNA ends persist and are recognized by ATP-bound OLD dimers via a positively charged channel across their ATPase subunits. ATP hydrolysis then activates OLD to cleave tRNAs, causing cytotoxicity. Single-cell microscopy reveals that dozens of OLD molecules associate with kilobases of adjacent DNA, amplifying the sparse physiological DNA end signal. Our findings reveal how an endogenous byproduct poses a constant autoimmune threat in bacteria, highlighting a universal molecular conflict across kingdoms and the convergent solutions evolved to resolve it.

microbiology↗

bioRxiv2025

Differential nucleosome organization in human interphase and metaphase chromosomes

DNA bendability plays a critical role in stabilizing nucleosome assembly, yet its contribution to nucleosome dynamics in vivo remains poorly understood. Here, we applied chemical mapping to generate high-resolution nucleosome positioning maps at single-base-pair resolution from human interphase and metaphase chromosomes, revealing distinct patterns of nucleosome organization between the two states. Notably, we observed a unifying pattern of nucleosome positioning near euchromatic landmarks, including promoters, enhancers, and insulators, during mitosis. Interphase nucleosomes exhibited extensive repositioning, marked by increased nucleosome density, reduced spacing between nucleosomes, and the appearance of additional fragile nucleosomes compared to metaphase. Furthermore, our results show that metaphase nucleosomes display significantly higher DNA cyclizability around the dyad axis, whereas interphase nucleosomes, particularly those near regulatory regions, tend to position DNA with greater cyclizability at the edges of the nucleosome. Together, these findings highlight a dynamic interplay between DNA mechanics and nucleosome organization during the cell cycle.

genomics↗

bioRxiv2025

Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli

Certain phages and microbes use Diversity-Generating Retroelements (DGRs) for targeted adaptation via a process called mutagenic retrohoming. This process relies on an error-prone reverse transcriptase that specifically misincorporates bases opposite adenines in the RNA template. The resulting mutagenized complementary DNA then integrates into a homologous target gene to introduce mutations at adenine residues. Although the functions of core DGR components are well-defined, we still dont know how other cellular factors influence their activity. To address this, we reconstituted the DGR from the Bordetella phage BPP-1 in Escherichia coli. Our systematic analysis uncovered several cellular factors that influence its activity. By sequencing the cDNA, we discovered the reverse transcriptase is particularly mutagenic in the 5-AAC-3 and 5-ACC-3 contexts, which explains their abundance in natural DGR templates. A transposon sequencing screen identified both positive and negative regulators, including the single-stranded DNA exonuclease ExoI, which unexpectedly inhibits DGR activity through a nuclease-independent mechanism. Using a massively parallel reporter assay, we found that DGR preferentially edits targets located near the replication origin and co-directionally oriented with replication. In the preferred orientation, the target sequence is located on the lagging-strand template, where the extended single-stranded DNA gap likely facilitates base pairing with the incoming complementary DNA. Collectively, these findings advance our understanding of how DGRs function within the cellular context and enabled a 1000-fold improvement in editing efficiency, establishing a foundation for future targeted-mutagenesis applications.

microbiology↗

bioRxiv2021

Do tigers hunt during the day? Diel Activity of the Asian tiger mosquito, Aedes albopictus (Diptera: Culicidae), in Urban and Suburban Habitats of North America

Aedes (Stegomyia) albopictus (Skuse) impacts human outdoor activity because of its aggressive biting behavior, and as a major vector of mosquito-borne diseases, it is also of public health importance. Although most mosquito species exhibit crepuscular activity by primarily host seeking at dawn and dusk, Ae. albopictus has been traditionally characterized as a diurnal or day-biting mosquito. With the global expansion and increased involvement of Ae. albopictus in mosquito-borne diseases, it is imperative to elucidate the diel activity of this species, particularly in newly invaded areas. Human sweep netting and carbon dioxide-baited rotator traps were used to evaluate the diel activity of Ae. albopictus in two study sites. Both trapping methods were used in New Jerseys Mercer County, USA (temperate urban), while only human sweep netting was used in Floridas Volusia County, USA (subtropical suburban). Human sweep netting was performed to determine adult mosquito activity at sunrise, solar noon, sunset, and lunar midnight. Because New Jersey is in a temperate area, diel activity was investigated during the early season (3-19 July), peak season (25 July-19 September), and late season (22 September-22 October). Aedes albopictus showed the highest activity during peak and late seasons at solar noon (P < 0.05). At sunrise and sunset during the peak season, Ae. albopictus activity was similar. Lunar midnight activity was significantly lower than sunrise and solar noon (P < 0.05) but was similar to that of sunset. In the late season, the highest activity was observed during solar noon while the least activity was observed during sunrise and lunar midnight (P<0.05). Rotator traps used in conjunction with the human sweep net technique exhibited similar results. Seasonal activity was not differentiated in Florida due to the consistent subtropical weather. The highest adult activity was observed at sunrise using human sweep netting but it was not significantly different from solar noon and sunset. The lowest adult activity was observed at lunar midnight; however, it was not significantly different from solar noon and sunset. These results provide evidence that the diel activity of Ae. albopictus, contrary to the common perception of its diurnal activity, is much more varied. Because of the involvement of the species in the transmission of debilitating mosquito-borne pathogens such as chikungunya, dengue, and Zika virus, coupled with its affinity to thrive in human peridomestic environments, our findings have global implications in areas where Ae. albopictus thrives. It also highlights the importance of behavioral studies of vector species which will not only help mosquito control professionals plan the timing of their control efforts but also provide empirical evidence against conventional wisdoms that may unjustly persist within public health stewards. Author SummaryThe Asian tiger mosquito, Aedes albopictus, is an invasive mosquito which is now established in at least 40 states in the USA. Lack of efficient surveillance and control methods against Ae. albopictus, in addition to human-aided accidental transportations, have played a great role in its rapid expansion. Although surveillance measures are becoming more systematic and effective, control of this species still poses a great challenge. Aedes albopictus is difficult to control in the larval stage because it primarily develops in artificial containers that are widespread in peridomestic habitats. These habitats are not only ubiquitous in these environments, they are also cryptic, inaccessible, and extremely difficult to control. Therefore, control of Ae. albopictus in these environments often relies on adult control measures which utilize insecticides dispersed through ultra-low volume equipment as a cold aerosol space spray. These adulticide applications are often conducted at night against endemic mosquito species which are primarily active between dawn and dusk. However, since Ae. albopictus has been traditionally classified as a day-biting mosquito, mosquito control specialists have had doubts about the efficacy of a nocturnal application against a diurnally active mosquito. These uncertainties about intervention efforts become even more important during public health outbreaks of mosquito-borne pathogens such as chikungunya, dengue, or Zika viruses when protection of public health is of paramount importance in peridomestic habitats. Our investigations provide evidence that Ae. albopictus exhibits activity throughout the day and night and that nighttime adulticide applications may indeed be effective against this species, and should not be disregarded.

ecology↗

bioRxiv2019

A low-cost and high-precision scanning electrochemical microscope built with open source tools

A low-cost Scanning Electrochemical Microscope (SECM) was built with a 0.6 pA current measurement capability potentiostat and submicron resolution motorized stage, using open source software and hardware tools. The high performance potentiostat with a Python graphical user interface was built based on an open source project. Arduino boards, stepper motors, a manual XY micromanipulator stage, 3D printed couplers and gears were used in building the motorized stage. An open source motor control software was used for moving the motorized stage with high precision. An inverted microscope was utilized for viewing a standard microelectrode while scanning. The setup was tested in the formation of a map of electrochemical signals from an array of pores on a parafilm membrane. As the setup will be used in future biosensing experiments, DNA hybridization detection experiments were also performed with the setup.

biochemistry↗