Investigating the Roles for Essential Genes in the Regulation of the Circadian Clock in Synechococcus elongatus Using CRISPR Interference

Circadian rhythms are found widely throughout nature where cyanobacteria are the simplest organisms, in which the molecular details of the clock have been elucidated. Circadian rhythmicity in cyanobacteria is carried out via the KaiA, KaiB, and KaiC core oscillator proteins that keep ~24 h time. A series of input and output proteins-CikA, SasA, and RpaA-regulate the clock by sensing environmental changes and timing rhythmic activities, including global rhythms of gene expression. Our previous work identified a novel set of KaiC-interacting proteins, some of which are encoded by genes that are essential for viability. To understand the relationship of these essential genes to the clock, we applied CRISPR interference (CRISPRi) which utilizes a deactivated Cas9 protein and single-guide RNA (sgRNA) to reduce the expression of target genes but not fully abolish their expression to allow for survival. Eight candidate genes were targeted, and strains were analyzed by quantitative real-time PCR (qRT-PCR) for reduction of gene expression, and rhythms of gene expression were monitored to analyze circadian phenotypes. Strains with reduced expression of SynPCC7942_0001, dnaN, which encodes for the β-clamp of the replicative DNA polymerase, or SynPCC7942_1081, which likely encodes for a KtrA homolog involved in K+ transport, displayed longer circadian rhythms of gene expression than the wild type. As neither of these proteins have been previously implicated in the circadian clock, these data suggest that diverse cellular processes, DNA replication and K+ transport, can influence the circadian clock and represent new avenues to understand clock function.

Roles for the Synechococcus elongatus RNA-Binding Protein Rbp2 in Regulating the Circadian Clock

The cyanobacterial circadian oscillator, consisting of KaiA, KaiB, and KaiC proteins, drives global rhythms of gene expression and compaction of the chromosome and regulates the timing of cell division and natural transformation. While the KaiABC posttranslational oscillator can be reconstituted in vitro, the Kai-based oscillator is subject to several layers of regulation in vivo. Specifically, the oscillator proteins undergo changes in their subcellular localization patterns, where KaiA and KaiC are diffuse throughout the cell during the day and localized as a focus at or near the pole of the cell at night. Here, we report that the CI domain of KaiC, when in a hexameric state, is sufficient to target KaiC to the pole. Moreover, increased ATPase activity of KaiC correlates with enhanced polar localization. We identified proteins associated with KaiC in either a localized or diffuse state. We found that loss of Rbp2, found to be associated with localized KaiC, results in decreased incidence of KaiC localization and long-period circadian phenotypes. Rbp2 is an RNA-binding protein, and it appears that RNA-binding activity of Rbp2 is required to execute clock functions. These findings uncover previously unrecognized roles for Rbp2 in regulating the circadian clock and suggest that the proper localization of KaiC is required for a fully functional clock in vivo.

Electroencephalography for predicting antidepressant treatment success: A systematic review and meta-analysis

BACKGROUND

Patients suffering from major depressive disorder (MDD) regularly experience non-response to treatment for their depressive episode. Personalized clinical decision making could shorten depressive episodes and reduce patient suffering. Although no clinical tools are currently available, machine learning analysis of electroencephalography (EEG) shows promise in treatment response prediction.

METHODS

With a systematic review and meta-analysis, we evaluated the accuracy of EEG for individual patient response prediction. Importantly, we included only prediction studies that used cross-validation. We used a bivariate model to calculate prediction success, as expressed by area-under the curve, sensitivity and specificity. Furthermore, we analyzed prediction success for separate antidepressant interventions.

RESULTS

15 studies with 12 individual patient samples and a total of 479 patients were included. Research methods varied considerably between studies. Meta-analysis of results from this heterogeneous set of studies resulted in an area under the curve of 0.91, a sensitivity of 83 % (95 % CI 74-89 %), and a specificity of 86 % (95 % CI 81-90 %). Classification performance did not significantly differ between treatments. Although studies were all internally validated, no externally validated studies have been reported. We found substantial risk of bias caused by methodological shortcomings such as non-independent feature selection, though performance of non-biased studies was comparable.

LIMITATIONS

Sample sizes were relatively small and no study used external validation, increasing the risk of overestimation of accuracy.

CONCLUSIONS

Electroencephalography can predict the response to antidepressant treatment with high accuracy. However, future studies with more rigorous validation are needed to produce a clinical tool to guide interventions in MDD.

PROSPERO REGISTRATION NUMBER

CRD42021268169.

Adapting Undergraduate Research to Remote Work to Increase Engagement

Demand for undergraduate research experiences typically outstrips the available laboratory positions, which could have been exacerbated during the remote work conditions imposed by the SARS-CoV-2/COVID-19 pandemic. This report presents a collection of examples of how undergraduates have been engaged in research under pandemic work restrictions. Examples include a range of projects related to fluid dynamics, cancer biology, nanomedicine, circadian clocks, metabolic disease, catalysis, and environmental remediation. Adaptations were made that included partnerships between remote and in-person research students and students taking on more data analysis and literature surveys, as well as data mining, computational, and informatics projects. In many cases, these projects engaged students who otherwise would have worked in traditional bench research, as some previously had. Several examples of beneficial experiences are reported, such as the additional time spent studying the literature, which gave students a heightened sense of project ownership, and more opportunities to integrate feedback into writing and research. Additionally, the more intentional and regular communication necessitated by remote work proved beneficial for all team members. Finally, online seminars and conferences have made participation possible for many more students, especially those at predominantly undergraduate institutions. Participants aim to adopt these beneficial practices in our research groups even after pandemic restrictions end.

A Vital Layer of Support: One Safety Net Hospital's Palliative Care Response to the Pandemic

Context: During the coronavirus disease 2019 (COVID-19) pandemic, New York City's public hospitals experienced a significant increase in the number of critically ill patients, especially from minority populations. The palliative care consult service at Bellevue Hospital, therefore, adjusted rapidly to meet the increased needs of our patients and colleagues. Objectives: To describe the dynamic palliative care needs during a public hospital's COVID-19 surge, including a process to utilize nonpalliative care trained volunteers to meet the increased demand for inpatient palliative care consults. Confronting the Challenge: Given the flexibility needed during the surge response, the consult team focused on three key elements to meet the system's needs: surge staffing, support, and scale. The consult service expanded into three individual teams to accommodate daily rounds with the medical intensive care and general medicine teams. Nonpalliative care trained community volunteers and internally redeployed providers received targeted training in advanced care planning and were subsequently embedded within the three teams, each led by a palliative care provider. A total of 12 volunteers joined the palliative care team. During eight weeks of the surge, the service cared for a total of 276 patients, 111 of whom were seen by volunteers. Over 50% of the palliative care patients had limited English proficiency. Conclusion: The inpatient palliative care consult service structure adapted rapidly in response to the increased need for advanced care planning and support throughout the hospital during the COVID-19 surge. Focusing on three key areas of surge staffing, support, and scale resulted in expert coordination with the hospital and system level leadership, efficient training of volunteer providers, and frequent re-evaluation of response strategies. These elements were vital in allowing the palliative care team to harness the expertise of various volunteer providers to meet the increased demands of a safety net hospital during the COVID-19 pandemic.

Development of an Outpatient Palliative Care Protocol to Monitor Fidelity in the Emergency Medicine Palliative Care Access Trial

Introduction: Palliative care is recommended for patients with life-limiting illnesses; however, there are few standardized protocols for outpatient palliative care visits. To address the paucity of data, this article aims to: (1) describe the elements of outpatient palliative care that are generalizable across clinical sites; (2) achieve consensus about standardized instruments used to assess domains within outpatient palliative care; and (3) develop a protocol and intervention checklist for palliative care clinicians to document outpatient visit elements that might not normally be recorded in the electronic heath record. Methods: As part of a randomized control trial of nurse-led telephonic case management versus specialty, outpatient palliative care in older adults with serious life-limiting illnesses in the Emergency Department, we assessed the structural characteristics of outpatient care clinics across nine participating health care systems. In addition, direct observation of outpatient palliative care visits, consultation from content experts, and survey data were used to develop an outpatient palliative care protocol and intervention checklist. Implementation: The protocol and checklist are being used to document the contents of each outpatient palliative care visit conducted as a part of the Emergency Medicine Palliative Care Access (EMPallA) trial. Variation across palliative care team staffing, clinic session capacity, and physical clinic model presents a challenge to standardizing the delivery of outpatient palliative care.

Structural basis of the day-night transition in a bacterial circadian clock

Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post-adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.

A Microfluidic Platform for Long-Term Monitoring of Algae in a Dynamic Environment

Culturing cells in microfluidic "lab-on-a-chip" devices for time lapse microscopy has become a valuable tool for studying the dynamics of biological systems. Although microfluidic technology has been applied to culturing and monitoring a diverse range of bacterial and eukaryotic species, cyanobacteria and eukaryotic microalgae present several challenges that have made them difficult to culture in a microfluidic setting. Here, we present a customizable device for the long-term culturing and imaging of three well characterized strains of cyanobacteria and microalgae. This platform has several advantages over agarose pads and demonstrates great potential for obtaining high quality, single-cell gene expression data of cyanobacteria and algae in precisely controlled, dynamic environments over long time periods.

Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.

Best practices for fluorescence microscopy of the cyanobacterial circadian clock

This chapter deals with methods of monitoring the subcellular localization of proteins in single cells in the circadian model system Synechococcus elongatus PCC 7942. While genetic, biochemical, and structural insights into the cyanobacterial circadian oscillator have flourished, difficulties in achieving informative subcellular imaging in cyanobacterial cells have delayed progress of the cell biology aspects of the clock. Here, we describe best practices for using fluorescent protein tags to monitor localization. Specifically, we address how to vet fusion proteins and overcome challenges in microscopic imaging of very small autofluorescent cells.

Medical repatriation at end of life: Barriers, facilitation, and fulfillment—A case-series study at a New York public hospital

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Background: Foreign-born cancer patients frequently desire to return to their home country at the end of life. However, many barriers can make this process challenging. We herein present our recent experience with such patients. Methods: We reviewed charts of terminal cancer patients (pts) who traveled to their homeland at the end of life. Pts’ age, diagnoses, co-morbidities, prior cancer-directed treatment, predicted survival, symptoms, code status, admissions within 4 weeks of travel, oxygen need were noted. Interval between decision to travel and travel date, events during travel, and feedback from families, if available were collected. Results: 17 charts (11 female, 6 male) were analyzed. Mean age was 60 years and the most common diagnosis was thoracic malignancy (70%, 12 pts). All pts had disseminated cancer and had received an average of 2 lines of cancer-directed therapy. All had progressive cancers with expected survival <6 months. All were under the care of medical oncologists, palliative care and social work. The mean interval between decision to travel and travel date was 9 days. 8 were hospitalized at least once in the 4 weeks prior to the day of travel and 6 were cared for as inpatients immediately prior to travel. 11 pts were receiving opioids for pain and 3 were oxygen-dependent. 10 had documented discussions regarding resuscitation and 9 were discharged with New York State out-of –hospital DNR forms. All were discharged with medical records, medication supply and provider contact information. Mean travel distance was 4,099 miles. Provider concerns for decompensation during travel included brain herniation (2), spinal cord compression (3), bleeding (1), and sepsis (2). 16 pts successfully completed their journey. 1 pt died en-route prior to boarding the aircraft. 12 pts/families provided positive feedback about the experience. Conclusions: Return to homeland is an important goal for many terminally ill cancer pts and should be a routine part of end-of-life discussions. Medical repatriation can be accomplished when conducted in a planned, well-coordinated manner. Insights from this review can help us create guidelines that can be readily applied to specific scenarios.

New discoveries linking transcription to DNA repair and damage tolerance pathways

In Escherichia coli, the transcription elongation factor NusA is associated with all elongating RNA polymerases where it functions in transcription termination and antitermination. Here, we review our recent results implicating NusA in the recruitment of DNA repair and damage tolerance mechanisms to sites of stalled transcription complexes.

Intrathecal fentanyl added to bupivacaine and morphine for cesarean delivery may induce a subtle acute opioid tolerance

BACKGROUND

Previous studies have demonstrated that the addition of intrathecal fentanyl to a spinal anesthetic for cesarean delivery improves intraoperative analgesia. However, intrathecal fentanyl may induce acute tolerance to opioids. The objective of this study was to investigate whether the addition of intrathecal fentanyl to spinal anesthesia with intrathecal morphine increases postoperative analgesic requirements and pain scores.

METHODS

In this randomized, double-blinded study, 40 women having elective cesarean delivery were enrolled. Patients received spinal anesthesia with hyperbaric bupivacaine 12 mg, morphine 200 μg, and fentanyl 0, 5, 10 or 25 μg. Each patient received intravenous patient-controlled analgesia morphine for 24h postoperatively. Outcome measures included postoperative morphine usage and pain scores, as well as intraoperative pain, nausea, hypotension and vasopressor use.

RESULTS

Total morphine use over the 24-h post-spinal study period was similar among the study groups (P=0.129). Postoperative pain scores were higher in patients receiving fentanyl 5, 10 and 25 μg compared to fentanyl 0 μg control group (P=0.003).

CONCLUSIONS

The study results suggest that intrathecal fentanyl may induce acute tolerance to intrathecal morphine. However, because there was no difference in postoperative analgesia requirement and the difference in pain scores was small, the clinical significance of this finding is uncertain.

The transcription elongation factor NusA is required for stress-induced mutagenesis in Escherichia coli

Stress-induced mutagenesis describes the accumulation of mutations that occur in nongrowing cells, in contrast to mutagenesis that occurs in actively dividing populations, and has been referred to as stationary-phase or adaptive mutagenesis. The most widely studied system for stress-induced mutagenesis involves monitoring the appearance of Lac(+) revertants of the strain FC40 under starvation conditions in Escherichia coli. The SOS-inducible translesion DNA polymerase DinB plays an important role in this phenomenon. Loss of DinB (DNA pol IV) function results in a severe reduction of Lac(+) revertants. We previously reported that NusA, an essential component of elongating RNA polymerases, interacts with DinB. Here we report our unexpected observation that wild-type NusA function is required for stress-induced mutagenesis. We present evidence that this effect is unlikely to be due to defects in transcription of lac genes but rather is due to an inability to adapt and mutate in response to environmental stress. Furthermore, we extended our analysis to the formation of stress-induced mutants in response to antibiotic treatment, observing the same striking abolition of mutagenesis under entirely different conditions. Our results are the first to implicate NusA as a crucial participant in the phenomenon of stress-induced mutagenesis.

Efficacy and tolerability of vildagliptin vs. pioglitazone when added to metformin: a 24-week, randomized, double-blind study

AIM

The aim of this study was to compare the efficacy and tolerability of vildagliptin vs. pioglitazone as add-on therapy in patients with type 2 diabetes inadequately controlled with metformin monotherapy.

METHODS

This 24-week, multicentre, double-blind, randomized, active-controlled study compared vildagliptin (100 mg daily, given as equally divided doses, n = 295) and pioglitazone (30 mg daily, given as a single q.d. dose, n = 281) in patients with inadequate glycaemic control (A1C 7.5-11%) while receiving a stable metformin dose (> or =1500 mg daily). The adjusted mean changes from baseline to study endpoint (AMDelta) in A1C, fasting plasma glucose (FPG), fasting lipids and body weight were compared by analysis of covariance.

RESULTS

When added to a stable dose of metformin (mean dose at baseline >2000 mg/day), both vildagliptin and pioglitazone decreased A1C (AMDelta = -0.9 +/- 0.1% and -1.0 +/- 0.1%, respectively) from identical baseline values (8.4 +/- 0.1%). The between-group difference in AMDelta A1C was 0.1 +/- 0.1%, and non-inferiority of vildagliptin to pioglitazone was established at both 0.4 and 0.3% margins for upper limit of the 95% confidence intervals. Pioglitazone decreased FPG (AMDelta = -2.1 +/- 0.1 mmol/l) to a greater extent than vildagliptin (AMDelta = -1.4 +/- 0.1 mmol/l), but only pioglitazone increased body weight (AMDelta = +1.9 +/- 0.2 kg: between-group difference = -1.6 +/- 0.3 kg, p < 0.001). Adverse events (AEs) were reported by 60% of vildagliptin-treated patients and by 56.4% of pioglitazone-treated patients; serious AEs were reported by 2.0 and 4.6% of patients receiving vildagliptin and pioglitazone respectively. Mild hypoglycaemia was reported by one patient (0.3%) in the vildagliptin group and by no patients receiving pioglitazone.

CONCLUSIONS

When added to metformin, the efficacy of vildagliptin is non-inferior to that of pioglitazone. The treatments were similarly well tolerated, but only pioglitazone increased body weight.

Local infiltration of epinephrine-containing lidocaine with bicarbonate reduces superficial bleeding and pain during labor epidural catheter insertion: a randomized trial

BACKGROUND

Superficial bleeding after labor epidural catheter placement is a common phenomenon. In addition to delaying securing the epidural catheter, it may loosen the adhesive catheter dressing. The primary aim of this study was to determine whether skin infiltration with epinephrine-containing rather than plain lidocaine reduces superficial bleeding after catheter placement. Secondary objectives were to determine whether adding epinephrine and/or sodium bicarbonate affected infiltration pain.

METHODS

After institutional review board approval and informed consent, 80 healthy women receiving epidural analgesia during labor were randomly assigned in a double-blind manner to four local anesthetic mixtures (n=20 in each group): group L: lidocaine 1.5%, group LB: lidocaine 1.5% with 8.4% sodium bicarbonate, group LE: lidocaine 1.5% with epinephrine 1:200000, and group LEB: lidocaine 1.5% with epinephrine 1:200000 and 8.4% sodium bicarbonate. Clinical endpoints included the amount of superficial bleeding at the catheter site, pain during local anesthetic infiltration and epidural catheter movement during labor.

RESULTS

Demographic data were similar among the groups. The addition of epinephrine to lidocaine significantly reduced superficial bleeding. Solutions containing epinephrine were well tolerated and caused no cardiovascular disturbances. The addition of epinephrine did not increase pain, while bicarbonate reduced it [verbal score (scale 0-10) 3.6+/-2.2 vs. 2.6+/-1.8; P=0.04]. There were no differences in epidural catheter movement among the groups; no catheters became displaced during labor.

CONCLUSION

Local infiltration of epinephrine-containing lidocaine before epidural catheter insertion reduces superficial bleeding and the addition of bicarbonate decreases pain during skin infiltration.

Y-family DNA polymerases in Escherichia coli

The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. Genetic and biochemical studies have revealed that umuC+ and its homolog dinB+ encode novel DNA polymerases with the ability to catalyze synthesis past DNA lesions that otherwise stall replication--a process termed translesion synthesis (TLS). Similar polymerases have been identified in nearly all organisms, constituting a new enzyme superfamily. Although typically viewed as unfaithful copiers of DNA, recent studies suggest that certain TLS polymerases can perform proficient and moderately accurate bypass of particular types of DNA damage. Moreover, various cellular factors can modulate their activity and mutagenic potential.

A survey of labor patient-controlled epidural anesthesia practice in California hospitals

BACKGROUND

Patient-controlled epidural analgesia (PCEA) offers many advantages over continuous epidural infusions for labor analgesia including fewer physician interventions, improved analgesia and satisfaction, and reduced local anesthetic doses. However, anesthesiologists have been slow to adopt this technique, first described in 1988. No previous studies have evaluated specific labor patient-controlled epidural analgesia practices in the United States. The aim of this study was to determine labor epidural and patient-controlled epidural analgesia practices among California hospitals.

METHODS

Following institutional review board exemption approval, an online survey was created using freeonlinesurveys.com. An anonymous survey was sent via e-mail to 230 California Society of Anesthesiologists' members chosen at random to represent their hospitals' labor analgesia practices.

RESULTS

We received 133 replies from the 230 survey requests sent, a 58% response rate. The median labor epidural rate among the hospitals involved was 65% (range 0-95%). Overall, only 25% of California hospitals use patient-controlled epidural analgesia for analgesia in labor, with greater use among hospitals with dedicated obstetric anesthesia coverage and larger numbers of deliveries. Reasons given for not using patient-controlled epidural analgesia include cost, clinician preference, safety concerns and the inconvenience of change.

CONCLUSIONS

Despite the potential advantages of patient-controlled epidural analgesia over continuous epidural infusions for labor analgesia, patient-controlled epidural analgesia has not been widely adopted in California hospitals. Education regarding this technique is needed to encourage its increased use.

“Ultra-light” patient-controlled epidural analgesia during labor: effects of varying regimens on analgesia and physician workload

BACKGROUND

Patient-controlled epidural analgesia (PCEA) offers many advantages over continuous epidural infusions for maintenance of labor analgesia. Some of these benefits may depend on the PCEA settings. This study evaluated several regimens for "ultra-light" (0.125%) PCEA with basal continuous infusion (CI) in labor with goals of minimizing physician interventions while providing good analgesia.

METHODS

Two hundred and twenty ASA I-II women receiving epidural analgesia during active labor (cervical dilation <5 cm) were randomly assigned in a double-blind manner to four treatment groups (n=30 in each). Analgesia was maintained with a PCEA/CI pump using bupivacaine 0.0625% + sufentanil 0.35 microg/mL. PCEA settings were: group A: CI 10 mL/h, PCEA bolus 6 mL, 8-min lockout; group B: CI 10 mL/h, PCEA bolus 12 mL, 16-min lockout; group C: CI 15 mL/h, PCEA bolus 6 mL, 8-min lockout; group D: CI 15 mL/h, PCEA bolus 12 mL, 16-min lockout.

RESULTS

In groups A, B, C and D, 76, 77, 75 and 85% of parturients respectively, required no physician rescue boluses. Pain scores were low and maternal satisfaction was high in all groups, with minimal differences among them. Spontaneous vaginal delivery occurred in 78% of patients overall, instrumental (forceps or vacuum) delivery in 10% and cesarean section in 12%.

CONCLUSIONS

These ultra-light PCEA regimens provided excellent analgesia with minimal physician workload and a high spontaneous delivery rate. Use of moderate to high-volume, ultra-light PCEA/CI techniques should facilitate provision of labor analgesia in busy obstetric units.