Clinically relevant mutations in regulatory regions of metabolic genes facilitate early adaptation to ciprofloxacin in Escherichia coli.

The genomic landscape associated with early adaptation to ciprofloxacin is poorly understood. Although the interplay between core metabolism and antimicrobial resistance is being increasingly recognized, mutations in metabolic genes and their biological role remain elusive. Here, we exposed Escherichia coli to increasing gradients of ciprofloxacin with intermittent transfer-bottlenecking and identified mutations in three non-canonical targets linked to metabolism including a deletion (tRNA-ArgΔ414-bp) and point mutations in the regulatory regions of argI (ARG box) and narU. Our findings suggest that these mutations modulate arginine and carbohydrate metabolism, facilitate anaerobiosis and increased ATP production during ciprofloxacin stress. Furthermore, mutations in the regulatory regions of argI and narU were detected in over 70% of sequences from clinical E. coli isolates and were overrepresented among ciprofloxacin-resistant isolates. In sum, we have identified clinically relevant mutations in the regulatory regions of metabolic genes as a central theme that drives physiological changes necessary for adaptation to ciprofloxacin stress.

Regulation of an RNA toxin-antitoxin system, SdsR-RyeA, by a small RNA GcvB.

The toxin-antitoxin (TA) system regulates many physiological processes in free-living bacteria. One such TA system in Escherichia coli comprises an RNA toxin SdsR and an antitoxin RyeA. An overabundance of SdsR is toxic to the cells. RyeA normalizes SdsR abundance and helps the cells to adapt to altered conditions. The current study showed that a novel small RNA (sRNA) regulator GcvB directly interacts with RyeA to maintain its abundance in the cells under normal or low pH conditions. The deletion of the gcvB allele in the E. coli chromosome resulted in a ∼3-fold decrease in intrabacterial RyeA accumulation. An ectopic expression of GcvB in ΔgcvB strain reinstated RyeA abundance to its normal level. Induction of GcvB in the cells upon exposure to low pH resulted in a simultaneous increase in intracellular RyeA. While GcvB increases RyeA abundance in the cells, SdsR accumulation is divergently regulated by GcvB. The absence of the gcvB gene in E. coli leads to upregulation of SdsR and vice versa. The GcvB-mediated decrease of SdsR accumulation stems from the increased RyeA-driven normalization of SdsR. This study delineates a novel mechanism for the regulation of the expression of an RNA toxin SdsR by another sRNA regulator GcvB through a feed-forward control.

Role of Yrn2 under oxidative stress in Deinococcus radiodurans.

Among the two Y RNAs in Deinococcus radiodurans, the functional properties of Yrn2 are still not known. Yrn2 although consists of a long stem-loop for Rsr binding, differs from Yrn1 in the effector binding site. An initial study on Yrn2 delineated it to be a UV-induced noncoding RNA. Apart from that Yrn2 has scarcely been investigated. In the current study, we identified Yrn2 as an γ-radiation induced Y RNA, which is also induced upon H2O2 and mitomycin treatment. Ectopically expressed Yrn2 appeared to be nontoxic to the cell growth. An overabundance of Yrn2 was found to ameliorate cell survival under oxidative stress through the detoxification of intracellular reactive oxygen species with a subsequent decrease in total protein carbonylation. A significant accumulation of intracellular Mn(II) with unaltered Fe(II) and Zn(II) with detected while Yrn2 is overabundant in the cells. This study identified the role of a novel Yrn2 under oxidative stress in D. radiodurans.

A novel ionizing radiation-induced small RNA, DrsS, promotes the detoxification of reactive oxygen species in Deinococcus radiodurans.

A plethora of gene regulatory mechanisms with eccentric attributes in Deinoccocus radiodurans confer it to possess a distinctive ability to survive under ionizing radiation. Among the many regulatory processes, small RNA (sRNA)-mediated regulation of gene expression is prevalent in bacteria but barely investigated in D. radiodurans. In the current study, we identified a novel sRNA, DrsS, through RNA-seq analysis in D. radiodurans cells while exposed to ionizing radiation. Initial sequence analysis for promoter identification revealed that drsS is potentially co-transcribed with sodA and dr_1280 from a single operon. Elimination of the drsS allele in D. radiodurans chromosome resulted in an impaired growth phenotype under γ-radiation. DrsS has also been found to be upregulated under oxidative and genotoxic stresses. Deletion of the drsS gene resulted in the depletion of intracellular concentration of both Mn2+ and Fe2+ by ~70% and 40%, respectively, with a concomitant increase in carbonylation of intracellular protein. Complementation of drsS gene in ΔdrsS cells helped revert its intracellular Mn2+ and Fe2+ concentration and alleviated carbonylation of intracellular proteins. Cells with deleted drsS gene exhibited higher sensitivity to oxidative stress than wild-type cells. Extrachromosomally expressed drsS in ΔdrsS cells retrieved its oxidative stress resistance properties by catalase-mediated detoxification of reactive oxygen species (ROS). In vitro binding assays indicated that DsrS directly interacts with the coding region of the katA transcript, thus possibly protecting it from cellular endonucleases in vivo. This study identified a novel small RNA DrsS and investigated its function under oxidative stress in D. radiodurans. IMPORTANCE: Deinococcus radiodurans possesses an idiosyncratic quality to survive under extreme ionizing radiation and, thus, has evolved with diverse mechanisms which promote the mending of intracellular damages caused by ionizing radiation. As sRNAs play a pivotal role in modulating gene expression to adapt to altered conditions and have been delineated to participate in almost all physiological processes, understanding the regulatory mechanism of sRNAs will unearth many pathways that lead to radioresistance in D. radiodurans. In that direction, DrsS has been identified to be a γ-radiation-induced sRNA, which is also induced by oxidative and genotoxic stresses. DrsS appeared to activate catalase under oxidative stress and detoxify intracellular ROS. This sRNA has also been shown to balance intracellular Mn(II) and Fe concentrations protecting intracellular proteins from carbonylation. This novel mechanism of DrsS identified in D. radiodurans adds substantially to our knowledge of how this bacterium exploits sRNA for its survival under stresses.

Underwater Adhesives from Redox-Responsive Polyplexes of Thiolated Polyamide Polyelectrolytes.

We report the fabrication of optically clear underwater adhesives using polyplexes of oppositely charged partially-thiolated polyamide polyelectrolytes (TPEs). The thiol content of the constituent PEs was varied to assess its influence on the adhesive properties of the resulting glues. These catechol-free, redox-responsive TPE-adhesives were formulated in aquo and exhibited high optical transparency and strong adhesion even on submerged or moist surfaces of diverse polar substrates such as glass, aluminium, wood, and bone pieces. The adhesives could be cured under water through oxidative disulphide crosslinking of the constituent TPEs. The polyamide backbone provided multi-site H-bonding interactions with the substrates while the disulphide crosslinking provided the cohesive strength to the glue. Strong adhesion of mammalian bones (load bearing capacity upto 7 kg/cm2 ) was achieved using the adhesive containing 30 mol % thiol residues. Higher pH and use of oxidants such as povidone-iodine solution enhanced the curing rate of the adhesives, and so did the use of Tris buffer instead of Phosphate buffer. The porous architecture of the adhesive and its progressive degradation in aqueous medium over the course of three weeks bode well for diverse biomedical applications where temporary adhesion of tissues is required.

Role of Interventional Radiology (IR) in vascular emergencies among cirrhotic patients.

Gastrointestinal hemorrhage remains one of the most common causes of morbidity and mortality among patients with liver cirrhosis. Mostly, these patients bleed from the gastroesophageal varices. However, nonvariceal bleeding is also more likely to occur in these patients. Because of frequent co-existing coagulopathy, cirrhotics are more prone to bleed from a minor vascular injury while performing percutaneous interventions. Ultrasound-guided bedside vascular access is an essential procedure in liver critical care units. Transjugular portosystemic shunts (TIPS) with/without variceal embolization is a life-saving measure in patients with refractory variceal bleeding. Whenever feasible, balloon-assisted retrograde transvenous obliteration (BRTO) is an alternative to TIPS in managing gastric variceal bleeding, but without a risk of hepatic encephalopathy. In cases of failed or unfeasible endotherapy, transarterial embolization using various embolic agents remains the cornerstone therapy in patients with nonvariceal bleeding such as ruptured hepatocellular carcinoma, gastroduodenal ulcer bleeding, and procedure-related hemorrhagic complications. Among various embolic agents, N-butyl cyanoacrylate (NBCA) enables better vascular occlusion in cirrhotics, even in coagulopathy, making it a more suitable embolic agent in an expert hand. This article briefly entails the different interventional radiological procedures in vascular emergencies among patients with liver cirrhosis.

Is salvage Plug-Assisted Retrograde Transvenous Obliteration (PARTO) safe and effective for bleeding gastric varices ?- A preliminary single-center experience.

BACKGROUND: Vascular plug-assisted retrograde transvenous obliteration (PARTO) obliterates the gastric varices and portosystemic shunt, thus resulting in a lower rebleeding rate than endoscopic glue/sclerotherapy. AIMS: To evaluate the safety and efficacy of PARTO as salvage therapy in liver cirrhosis with gastric variceal bleed (GVB) after failed endotherapy. We assessed the clinical success rate and changes in liver function at 6- months. MATERIALS AND METHODS: Patients who underwent salvage PARTO after failed endotherapy for GVB (between December 2021 and November 2022) were searched and analyzed from the hospital database. Clinical success rate and rebleed rate were obtained at six months. Child-Pugh score (CTP) and Model for end-stage liver disease (MELD) score were calculated and compared between baseline and 6-month follow-up. RESULTS: Fourteen patients (n = 14, Child-Pugh class A/B) underwent salvage PARTO. Nine had GOV-2, and five had IGV-1 varices. The mean shunt diameter was 11.6 ± 1.6 mm. The clinical success rate of PARTO was 100% (no recurrent gastric variceal hemorrhage within six months). No significant deterioration in CTP (6.79 ± 0.98 vs. 6.21 ± 1.52; p = 0.12) and MELD scores (11.5 ± 4.05 vs. 10.21 ± 3.19; p = 0.36) was noted at 6 months. All patients were alive at 6 months. One patient (n = 1, 7.1%) bled from esophageal varices after three days of PARTO and was managed with variceal banding. 21.4% (3/14) patients had progression of esophageal varices at 6 months requiring prophylactic band ligation. Three patients (21.4%) had new onset or worsening ascites and responded to low-dose diuretics therapy. CONCLUSIONS: PARTO is a safe and effective procedure for bleeding gastric varices without any deterioration in liver function even after six months. Patient selection is critical to prevent complications. Further prospective studies with larger sample size are required to validate our findings.

Patterning at the Resolution Limit of Commercial Electron Beam Lithography.

It has been long known that low molecular weight resists can achieve a very high resolution, theoretically close to the probe diameter of the electron beam lithography (EBL) system. Despite technological improvements in EBL systems, the advances in resists have lagged behind. Here we demonstrate that a low-molecular-mass single-source precursor resist (based on cadmium(II) ethylxanthate complexed with pyridine) is capable of a achieving resolution (4 nm) that closely matches the measured probe diameter (∼3.8 nm). Energetic electrons enable the top-down radiolysis of the resist, while they provide the energy to construct the functional material from the bottom-up─unit cell by unit cell. Since this occurs only within the volume of resist exposed to primary electrons, the minimum size of the patterned features is close to the beam diameter. We speculate that angstrom-scale patterning of functional materials is possible with single-source precursor resists using an aberration-corrected electron beam writer with a spot size of ∼1 Å.

Synthesis and characterization of zinc derivatized 3, 5-dihydroxy 4', 7-dimethoxyflavone and its anti leishmaniasis activity against Leishmania donovani.

This study reports the synthesis and characterization of zinc derivatized 3,5-dihydroxy 4', 7- dimethoxyflavone (DHDM-Zn) compound for the development of new antileishmanial agents. The interaction studies of DHDM with zinc were carried out by UV spectra and fluorescence spectra analysis. Characterization of the complex was further accomplished by multi-spectroscopic techniques such as FTIR, Raman, HRMS, NMR, FESEM-EDX. The morphological and topographical studies of synthesized DHDM-Zn were carried out using FESEM with EDX. Further, it was demonstrated that DHDM-Zn exhibited an excellent in vitro antagonistic effect against the promastigote form of L. donovani. In addition, the possible mechanisms of promastigote L. donovani cell death, by involvement of derivatized compound in arrest of the cell cycle in the G1 phase and residual cell count reduction were investigated. Promastigote growth kinetics performed in the presence of the derivatized compound revealed a slow growth rate. The combination of growth kinetics and cell cycle analysis, made it possible to interpret and classify the cause of leishmanial cell death accurately. These results support that zinc derivatized complex (DHDM-Zn) might work as a lead compound for designing and developing a new antileishmanial drug.

Angstrom-Scale Transparent Overcoats: Interfacial Nitrogen-Driven Atomic Intermingling Promotes Lubricity and Surface Protection of Ultrathin Carbon.

Lubricity, a phenomenon which enables the ease of motion of objects, and wear resistance, which minimizes material damage or degradation, are important fundamental characteristics for sustainable technology developments. Ultrathin coatings that promote lubricity and wear resistance are of huge importance for a number of applications, including magnetic storage and micro-/nanoelectromechanical systems. Conventional ultrathin coatings have, however, reached their limit. Graphene-based materials that have shown promise to reduce friction and wear have many intrinsic limitations such as high temperature and substrate-specific growth. To address these concerns, a great deal of research is currently ongoing to optimize graphene-based materials. Here we discover that angstrom-thick carbon (8 Å) significantly reduces interfacial friction and wear. This lubricant shows ultrahigh optical transparency and can be directly deposited on a wide range of surfaces at room temperature. Experiments combined with molecular dynamics simulations reveal that the lubricating efficacy of 8 Å carbon is further improved via interfacial nitrogen.

Overexpression and repression of key rate-limiting enzymes (acetyl CoA carboxylase and HMG reductase) to enhance fatty acid production from Rhodotorula mucilaginosa.

Implementing two-way strategies to enhance the lipid production in Rhodotorula mucilaginosa with the help of metabolic engineering was focused on the overexpression of acetyl coenzyme A carboxylase (ACC1 carboxylase) gene and repression of 3-hydroxy 3-methylglutaryl reductase (HMG-CoA reductase). Using an inducer (sodium citrate) and inhibitor (rosuvastatin), the amounts of biomass, lipid, and carotenoid were estimated. In the presence of inhibitor (200 mM), 62% higher lipid concentration was observed, while 44% enhancement was recorded when inducer (3 mM) was used. A combination of both inhibitor and inducer resulted in a 57% increase in lipid concentration by the oleaginous yeast. These results were again confirmed by real-time polymerase chain reaction by targeting the expression of the genes coding for ACC1 carboxylase and 13-fold increase was recorded in the presence of inducer as compared with control. This combined strategy (inducer and inhibitor use) has been reported for the first time as far as the best of our knowledge. The metabolic engineering strategies reported here will be a powerful approach for the enhanced commercial production of lipids.

Slippery and Wear-Resistant Surfaces Enabled by Interface Engineered Graphene.

Friction and wear remain the primary cause of mechanical energy dissipation and system failure. Recent studies reveal graphene as a powerful solid lubricant to combat friction and wear. Most of these studies have focused on nanoscale tribology and have been limited to a few specific surfaces. Here, we uncover many unknown aspects of graphene's contact-sliding at micro- and macroscopic tribo-scales over a broader range of surfaces. We discover that graphene's performance reduces for surfaces with increasing roughness. To overcome this, we introduce a new type of graphene/silicon nitride (SiNx, 3 nm) bilayer overcoats that exhibit superior performance compared to native graphene sheets (mono and bilayer), that is, display the lowest microscale friction and wear on a range of tribologically poor flat surfaces. More importantly, two-layer graphene/SiNx bilayer lubricant (<4 nm in total thickness) shows the highest macroscale wear durability on tape-head (topologically variant surface) that exceeds most previous thicker (∼7-100 nm) overcoats. Detailed nanoscale characterization and atomistic simulations explain the origin of the reduced friction and wear arising from these nanoscale coatings. Overall, this study demonstrates that engineered graphene-based coatings can outperform conventional coatings in a number of technologies.

A novel mechanism of RyeA/SraC induction under acid stress.

RyeA/SraC is a cis-encoded small RNA (sRNA), which act as an anti-toxin to RpoS-regulated RyeB toxin in Escherichia coli. Ectopic expression of RyeA was reported to diminish the RyeB accumulation by serving as a RNA trap. Lower abundance of RyeA in the early exponential growth phase turned out to be the outcome of its degradation by RNase BN/Z. In the current study, we show that RyeA is an acid stress inducible sRNA, and global stress responsive factor RpoS appeared to be inessential in RyeA induction. Although, ryeB-pphA dicistronic transcript at low pH condition was stimulated by ∼4-fold, however, RyeB population was found to be decreased by > 50% under the same condition by the decoy action of enhanced RyeA accumulation. Investigation of the mechanism of RyeA induceduction at low pH in the exponential phase, revealed that RNase BN/Z, which catabolizes RyeA in the exponential phase, appeared to be highly sensitive to low pH stress. Both mRNA and protein level of RNase BN transpired to be decreased to <10% of their initial population. The expression of RyeA under acid stress is regulated by a feed-forward mechanism to normalize the RyeB profusion.

Regulation of RyeA/SraC expression in Escherichia coli.

Small RNAs (sRNAs) play a central role in regulating almost all physiological processes in bacteria. Majority of those sRNAs base pair with their targets and modulate their expressions. RyeA, previously known as SraC in Escherichia coli, is transcribed from a DNA strand complementary to the one from which another stationary phase induced sRNA RyeB/SdsR is synthesised. RyeA and RyeB in the stationary phase constitute a toxin-antitoxin system where RyeA normalizes accumulation of RyeB toxin by acting as RNA sponge. Aside from that, no more information is known about the regulation of RyeA expression. In the current study, we have systematically investigated the regulation of RyeA expression in different growth phases, and identified that RyeA expression is regulated neither by stationary phase-specific σ-factor nor by RNA chaperon Hfq. A dual function ribonuclease RNase BN mitigate its expression in the exponential phase. Thus, deletion of rbn gene promoted the stability of RyeA in the exponential phase. Conversely, RyeB in the stationary phase act as RNA decoy leading to RyeA degradation, and consequently, the preclusion of RyeB in the E. coli genome elevated RyeA. These regulatory mechanisms will help identify the primary role of RyeA in E. coli.

Quantification of Mixed Bloch-Néel Topological Spin Textures Stabilized by the Dzyaloshinskii-Moriya Interaction in Co/Pd Multilayers.

The three-dimensional structure of nanoscale topological spin textures stabilized by the Dzyaloshinskii-Moriya interaction is governed by the delicate competition between the exchange, demagnetization, and anisotropy energies. The quantification of such spin textures through direct experimental methods is crucial towards understanding the fundamental physics associated with their ordering, as well as their manipulation in spintronic devices. Here, we extend the Lorentz transmission electron microscopy technique to quantify mixed Bloch-Néel chiral spin textures stabilized by the Dzyaloshinskii-Moriya interaction in Co/Pd multilayers. Analysis of the observed intensities under varied imaging conditions coupled to corroborative micromagnetic simulations yields vital parameters that dictate the stability and properties of the complex spin texture, namely, the degree of mixed Bloch-Néel character, the domain wall width, the strength of the Dzyaloshinskii-Moriya interaction, and the exchange stiffness. This approach provides the necessary framework for the application of quantitative Lorentz phase microscopy to a broad array of topological spin systems.

Growth Phase-dependent Variation of RNase BN/Z Affects Small RNAs: REGULATION OF 6S RNA.

RNase BN, the RNase Z family member in E. coli, can participate in the processing of tRNA precursors. However, this function only becomes apparent when other processing enzymes are absent, raising the question of its primary physiological role. Here, we show that RNase BN itself is subject to growth phase-dependent regulation, because both rbn mRNA and RNase BN protein are at their highest levels in early exponential phase, but then decrease dramatically and are essentially absent in stationary phase. As a consequence of this variation, certain small RNAs, such as 6S RNA, remain low in exponential phase cells, and increase greatly in stationary phase. RNase BN affects 6S RNA abundance by decreasing its stability in exponential phase. RNase BN levels increase rapidly as cells exit stationary phase and are primarily responsible for the decrease in 6S RNA that accompanies this process. Purified RNase BN directly cleaves 6S RNA as shown by in vitro assays, and the 6S RNA:pRNA duplex is an even more favorable substrate of RNase BN. The exoribonuclease activity of RNase BN is unnecessary because all its action on 6S RNA is due to endonucleolytic cleavages. These data indicate that RNase BN plays an important role in determining levels of the global transcription regulator, 6S RNA, throughout the growth cycle.

Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-stranded RNA.

3' repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1.

How a CCA sequence protects mature tRNAs and tRNA precursors from action of the processing enzyme RNase BN/RNase Z.

In many organisms, 3' maturation of tRNAs is catalyzed by the endoribonuclease, RNase BN/RNase Z, which cleaves after the discriminator nucleotide to generate a substrate for addition of the universal CCA sequence. However, tRNAs or tRNA precursors that already contain a CCA sequence are not cleaved, thereby avoiding a futile cycle of removal and readdition of these essential residues. We show here that the adjacent C residues of the CCA sequence and an Arg residue within a highly conserved sequence motif in the channel leading to the RNase catalytic site are both required for the protective effect of the CCA sequence. When both of these determinants are present, CCA-containing RNAs in the channel are unable to move into the catalytic site; however, substitution of either of the C residues by A or U or mutation of Arg(274) to Ala allows RNA movement and catalysis to proceed. These data define a novel mechanism for how tRNAs are protected against the promiscuous action of a processing enzyme.

Transcriptional activation of the Mycobacterium tuberculosis virulence-associated small RNA MTS1338 by the response regulators DosR and PhoP.

MTS1338, a distinctive small RNA in pathogenic mycobacteria, plays a crucial role in host-pathogen interactions during infection. Mycobacterial cells encounter heterogeneous stresses in macrophages, which highly upregulate MTS1338. A dormancy regulatory factor DosR regulates the intracellular abundance of MTS1338. Herein, we investigated the interplay of DosR and a low pH-inducible gene regulator PhoP binding to the MTS1338 promoter. We identified that DosR strongly binds to two regions upstream of the MTS1338 gene. The proximal region possesses a threefold higher affinity than the distal site, but the presence of both regions increased the affinity for DosR by > 10-fold. PhoP did not bind to the MTS1338 gene but binds to the DosR-bound MTS1338 gene, suggesting a concerted mechanism for MTS1338 expression.