Life detection in a universe of false positives: Can the Fatal Flaws of Exoplanet Biosignatures be Overcome Absent a Theory of Life?

Astrobiology aims to determine the distribution and diversity of life in the universe. But as the word "biosignature" suggests, what will be detected is not life itself, but an observation implicating living systems. Our limited access to other worlds suggests this observation is more likely to reflect out-of-equilibrium gasses than a writhing octopus. Yet, anything short of a writhing octopus will raise skepticism about what has been detected. Resolving that skepticism requires a theory to delineate processes due to life and those due to abiotic mechanisms. This poses an existential question for life detection: How do astrobiologists plan to detect life on exoplanets via features shared between non-living and living systems? We argue that you cannot without an underlying theory of life. We illustrate this by analyzing the hypothetical detection of an "Earth 2.0" exoplanet. Without a theory of life, we argue the community should focus on identifying unambiguous features of life via four areas: examining life on Earth, building life in the lab, probing the solar system, and searching for technosignatures. Ultimately, we ask, what exactly do astrobiologists hope to learn by searching for life?

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles.

Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.

Oxidized Phospholipid oxPAPC Alters Regulatory T-Cell Differentiation and Decreases Their Protective Function in Atherosclerosis in Mice.

BACKGROUND: Regulatory T cells (Tregs) are protective in atherosclerosis but reduced during disease progression due to cell death and loss of stability. However, the mechanisms of Treg dysfunction remain unknown. Oxidized phospholipids are abundant in atherosclerosis and can activate innate immune cells, but little is known regarding their impact on T cells. Given Treg loss during atherosclerosis progression and oxidized phospholipid levels in the plaque microenvironment, we investigated whether oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (oxPAPC), an oxidized phospholipid associated with atherosclerotic plaques, alters Treg differentiation and function. METHODS: CD4+ T cells were polarized to Treg, T helper (Th) 1, and Th17 cells with or without oxPAPC and assessed by flow cytometry. Gene expression in oxPAPC-treated Tregs was analyzed by bulk RNA sequencing. Functional studies of oxPAPC-induced Tregs were performed by coculturing Tregs with CellTrace Violet-labeled cells in vitro, and by adoptively transferring Tregs to hyperlipidemic Ldlr-/- mice to measure atherosclerosis progression. RESULTS: Compared with controls, oxPAPC-treated Tregs were less viable, but surviving cells expressed higher levels of the Th1-associated markers T-bet, CXCR3, and IFN (interferon)-γ. Th1 and Th17 skewing cultures were unaltered by oxPAPC. IFN-γ is linked to Treg instability, thus Treg polarization experiments were repeated using Ifngr1-/- CD4+ T cells. IFNγR1 (INF gamma receptor 1) deficiency did not improve cell viability in oxPAPC-treated Tregs; however, T-bet and IFN-γ expression was not increased in surviving cells suggesting a role for IFN-γsignaling. OxPAPC-treated Tregs were less suppressive in vitro, and adoptive transfer studies in hyperlipidemic Ldlr-/- mice showed that oxPAPC-induced Tregs possessed altered tissue homing and were insufficient to inhibit atherosclerosis progression. CONCLUSIONS: OxPAPC elicits Treg-specific changes altering Treg differentiation and inducing a Th1-like phenotype in surviving cells partially through IFN-γ signaling. This is biologically relevant as oxPAPC-treated Tregs do not reduce atherosclerosis progression in Ldlr-/- mice. This study supports the role of oxidized phospholipids in negatively impacting Treg differentiation and atheroprotective function.

RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes.

Mutations in RanBP2 (also known as Nup358), one of the main components of the cytoplasmic filaments of the nuclear pore complex, contribute to the overproduction of acute necrotizing encephalopathy (ANE1)-associated cytokines. Here we report that RanBP2 represses the translation of the interleukin 6 (IL6) mRNA, which encodes a cytokine that is aberrantly up-regulated in ANE1. Our data indicates that soon after its production, the IL6 messenger ribonucleoprotein (mRNP) recruits Argonautes bound to let-7 microRNA. After this mRNP is exported to the cytosol, RanBP2 sumoylates mRNP-associated Argonautes, thereby stabilizing them and enforcing mRNA silencing. Collectively, these results support a model whereby RanBP2 promotes an mRNP remodelling event that is critical for the miRNA-mediated suppression of clinically relevant mRNAs, such as IL6.

HDAC Inhibition Reverses Preexisting Diastolic Dysfunction and Blocks Covert Extracellular Matrix Remodeling.

BACKGROUND: Diastolic dysfunction (DD) is associated with the development of heart failure and contributes to the pathogenesis of other cardiac maladies, including atrial fibrillation. Inhibition of histone deacetylases (HDACs) has been shown to prevent DD by enhancing myofibril relaxation. We addressed the therapeutic potential of HDAC inhibition in a model of established DD with preserved ejection fraction. METHODS: Four weeks after uninephrectomy and implantation with deoxycorticosterone acetate pellets, when DD was clearly evident, 1 cohort of mice was administered the clinical-stage HDAC inhibitor ITF2357/Givinostat. Echocardiography, blood pressure measurements, and end point invasive hemodynamic analyses were performed. Myofibril mechanics and intact cardiomyocyte relaxation were assessed ex vivo. Cardiac fibrosis was evaluated by picrosirius red staining and second harmonic generation microscopy of left ventricle (LV) sections, RNA sequencing of LV mRNA, mass spectrometry-based evaluation of decellularized LV biopsies, and atomic force microscopy determination of LV stiffness. Mechanistic studies were performed with primary rat and human cardiac fibroblasts. RESULTS: HDAC inhibition normalized DD without lowering blood pressure in this model of systemic hypertension. In contrast to previous models, myofibril relaxation was unimpaired in uninephrectomy/deoxycorticosterone acetate mice. Furthermore, cardiac fibrosis was not evident in any mouse cohort on the basis of picrosirius red staining or second harmonic generation microscopy. However, mass spectrometry revealed induction in the expression of >100 extracellular matrix proteins in LVs of uninephrectomy/deoxycorticosterone acetate mice, which correlated with profound tissue stiffening based on atomic force microscopy. ITF2357/Givinostat treatment blocked extracellular matrix expansion and LV stiffening. The HDAC inhibitor was subsequently shown to suppress cardiac fibroblast activation, at least in part, by blunting recruitment of the profibrotic chromatin reader protein BRD4 (bromodomain-containing protein 4) to key gene regulatory elements. CONCLUSIONS: These findings demonstrate the potential of HDAC inhibition as a therapeutic intervention to reverse existing DD and establish blockade of extracellular matrix remodeling as a second mechanism by which HDAC inhibitors improve ventricular filling. Our data reveal the existence of pathophysiologically relevant covert or hidden cardiac fibrosis that is below the limit of detection of histochemical stains such as picrosirius red, highlighting the need to evaluate fibrosis of the heart using diverse methodologies.

TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes.

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

Natural trajectory of recovery of COVID-19 associated olfactory loss.

IMPORTANCE: Prevalence of post-viral olfactory loss has increased dramatically due to the frequency and severity of olfactory dysfunction associated with infection by the SARS-CoV-2 virus. OBJECTIVE: To determine the trajectory of COVID-19 olfactory loss over a six-month period. A key secondary objective is to assess predictive factors associated with the recovery of olfaction. DESIGN: Longitudinal repeated-measures study that enrolled from May 5, 2020 to February 2, 2021, with the last date of data collection on June 15, 2021. SETTING: Barnes-Jewish HealthCare/Washington University School of Medicine facilities (Saint Louis, Missouri, USA). PARTICIPANTS: Individuals who tested positive for SARS-CoV-2 by real-time polymerase chain reaction on nasopharyngeal swab and indicated olfactory loss on COVID-19 screening questionnaire. Individuals were excluded if they had previously diagnosed history of olfactory loss, neurodegenerative disorders, <18 years of age, admitted to hospital service, unable to read, write, and understand English, or lacked computer or internet access. INTERVENTIONS/EXPOSURES: Watch and wait for spontaneous recovery. MAIN OUTCOME(S) AND MEASURE(S): Participants completed olfactory assessments every 30 days for six months. Each assessment consisted of the University of Pennsylvania Smell Identification Test (UPSIT), an objective "scratch-and-sniff" test, and Clinical Global Impressions (CGI), a subjective Likert rating scale. RESULTS: The mean age was 41 years old (SD = 16). 39 (80 %) were female and 42 (86 %) white. At baseline assessment of objective olfaction, 18 (36 %) participants had anosmia or severe hyposmia. Subjective, complete recovery at six months was 81 % (95 % CI 74 % to 88 %). Likelihood of recovery was associated with age <50 years (aHR = 8.1 (95 % CI 1.1 to 64.1)) and mild olfactory loss at baseline (UPSIT = 30-33 for males and 31-34 for females) (aHR 6.2 (95 % CI 1.2 to 33.0)). CONCLUSIONS AND RELEVANCE: The trajectory of olfactory recovery among adults with COVID-19 olfactory loss illustrated rapid recovery within 2-3 weeks of infection, and by six months 81 % had recovered based on self-report. Age <50 years old and mild severity of olfactory loss at baseline were associated with increased likelihood of recovery of olfaction. These findings can be used to inform shared decision-making with patients.

Dynamic Chromatin Targeting of BRD4 Stimulates Cardiac Fibroblast Activation.

RATIONALE: Small molecule inhibitors of the acetyl-histone binding protein BRD4 have been shown to block cardiac fibrosis in preclinical models of heart failure (HF). However, since the inhibitors target BRD4 ubiquitously, it is unclear whether this chromatin reader protein functions in cell type-specific manner to control pathological myocardial fibrosis. Furthermore, the molecular mechanisms by which BRD4 stimulates the transcriptional program for cardiac fibrosis remain unknown. OBJECTIVE: We sought to test the hypothesis that BRD4 functions in a cell-autonomous and signal-responsive manner to control activation of cardiac fibroblasts, which are the major extracellular matrix-producing cells of the heart. METHODS AND RESULTS: RNA-sequencing, mass spectrometry, and cell-based assays employing primary adult rat ventricular fibroblasts demonstrated that BRD4 functions as an effector of TGF-ß (transforming growth factor-ß) signaling to stimulate conversion of quiescent cardiac fibroblasts into Periostin (Postn)-positive cells that express high levels of extracellular matrix. These findings were confirmed in vivo through whole-transcriptome analysis of cardiac fibroblasts from mice subjected to transverse aortic constriction and treated with the small molecule BRD4 inhibitor, JQ1. Chromatin immunoprecipitation-sequencing revealed that BRD4 undergoes stimulus-dependent, genome-wide redistribution in cardiac fibroblasts, becoming enriched on a subset of enhancers and super-enhancers, and leading to RNA polymerase II activation and expression of downstream target genes. Employing the Sertad4 (SERTA domain-containing protein 4) locus as a prototype, we demonstrate that dynamic chromatin targeting of BRD4 is controlled, in part, by p38 MAPK (mitogen-activated protein kinase) and provide evidence of a critical function for Sertad4 in TGF-ß-mediated cardiac fibroblast activation. CONCLUSIONS: These findings define BRD4 as a central regulator of the pro-fibrotic cardiac fibroblast phenotype, establish a p38-dependent signaling circuit for epigenetic reprogramming in heart failure, and uncover a novel role for Sertad4. The work provides a mechanistic foundation for the development of BRD4 inhibitors as targeted anti-fibrotic therapies for the heart.

Surgical procedures for male infertility: an update.

PURPOSE OF REVIEW: The aim of this review is to provide an overview of surgical treatment options for male infertility including varicocelectomy, treatment of ejaculatory duct obstruction, vasovasostomy, and sperm extraction, and to review recent advances in techniques and technologies that may improve operative outcomes. RECENT FINDINGS: Microscopic subinguinal varicocelectomy has been shown to have the highest success rates with lowest rates of complications, and may be facilitated by the use of Doppler, indocyanine green angiography, and the 4K3D operating video microscope. The standard treatment for ejaculatory duct obstruction by transurethral resection of the ejaculatory ducts has changed little over time, but vesiculoscopy may allow for temporary dilation of an obstruction to allow for natural conception, while also offering diagnostic capabilities. Use of the robotic platform has gained popularity for vasectomy reversals but controversy remains regarding the cost-effectiveness of this option. Recently, a reinforcing suture technique has been described for vasovasostomy to minimize anastomotic breakdown and reversal failure. Finally, gray-scale and color-enhanced ultrasound may improve ability to predict successful sperm retrieval during extraction procedures. SUMMARY: Though the fundamentals of surgical treatment options for male infertility have changed little with time, technological advancements have contributed to improved surgical outcomes over recent years.

Assessment of complications following urinary diversion for benign indications.

INTRODUCTION: To evaluate complications following urinary diversion for non-malignant conditions. MATERIALS AND METHODS: We performed a retrospective review of patients undergoing urinary diversion for benign indications between 2000 and 2017. Data collected including patient demographic and clinical characteristics, surgical characteristics, and complications. Complications were graded using Clavien-Dindo classification and were categorized as early versus delayed (≤ versus > 90 day postoperatively). Logistic regression assessed for predictors of developing any postoperative complication. RESULTS: A total of 68 patients were identified for study analysis with median follow up of 24 (7-72) months. Sixty-eight and 25% of patients underwent diversion for neurogenic bladder and complications related to pelvic radiation, respectively. A majority (90%) underwent ileal conduit with the remainder undergoing continent diversion. A total of 121 complications were identified, comprising 50 early and 72 delayed. Overall, 77% of patients had at least one complication during the follow up period. Fifty-one percent of patients experienced early complication, while 66% of patients experienced delayed complications. Complications of Clavien-Dindo Score ≥ IIIB were seen in 48% of patients. The most common early complication was wound infection (12%); delayed was urinary tract infection (39%). Multivariable logistic regression modeling found no independent predictors of complication, although the best-fit model included BMI, diabetes, presence of multiple comorbidities, and operative time (hr) as positive predictors of complication. CONCLUSION: Our study demonstrates that urinary diversion for benign etiologies is associated with a significant rate of complication. A large percentage of these complications occur in the delayed period and are classified as severe complications.

Sperm agglutination: Prevalence and contributory factors.

Agglutination is a finding noted in semen analyses (SAs) that often causes confusion as to its significance. While some have attributed agglutination to antisperm antibodies (ASAs), there are other causes as well, such as genital tract infection and ascorbic acid deficiency. Additionally, it is known that patients with ASAs often have risk factors such as a history of scrotal trauma or surgery. Therefore, we sought to determine the prevalence of agglutination in our patient population and correlate it with these risk factors, regardless of the presence/absence of ASAs. A retrospective study was conducted on the SAs of men seen at a single academic Reproductive Center. Of the 1,095 SAs identified, 133 (12.1%) patients experienced agglutination (61.7% scant, 21.8% moderate and 16.5% excessive). Of patients who underwent multiple SAs, 24 (12.2%) showed variability. Furthermore, patients who underwent scrotal surgery carried 3.4 times the risk of agglutination (X2 p < 0.01) and 5.5 times the risk of variability (X2 p < 0.01) as compared to those patients without a history significant for scrotal surgery. Agglutination is a relatively common finding in men presenting to a reproductive clinic with little intrapatient variability. Scrotal surgery confers a higher risk of agglutination and variability.

Criticality Distinguishes the Ensemble of Biological Regulatory Networks.

The hypothesis that many living systems should exhibit near-critical behavior is well motivated theoretically, and an increasing number of cases have been demonstrated empirically. However, a systematic analysis across biological networks, which would enable identification of the network properties that drive criticality, has not yet been realized. Here, we provide a first comprehensive survey of criticality across a diverse sample of biological networks, leveraging a publicly available database of 67 Boolean models of regulatory circuits. We find all 67 networks to be near critical. By comparing to ensembles of random networks with similar topological and logical properties, we show that criticality in biological networks is not predictable solely from macroscale properties such as mean degree ⟨K⟩ and mean bias in the logic functions ⟨p⟩, as previously emphasized in theories of random Boolean networks. Instead, the ensemble of real biological circuits is jointly constrained by the local causal structure and logic of each node. In this way, biological regulatory networks are more distinguished from random networks by their criticality than by other macroscale network properties such as degree distribution, edge density, or fraction of activating conditions.

Stereopermutation on the Putative Structure of the Marine Natural Product Mucosin.

A stereodivergent total synthesis has been executed based on the plausibly misassigned structure of the unusual marine hydrindane mucosin (1). The topological connectivity of the four contiguous all-carbon stereocenters has been examined by selective permutation on the highlighted core. Thus, capitalizing on an unprecedented stereofacial preference of the cis-fused bicycle[4.3.0]non-3-ene system when a Michael acceptor motif is incorporated, copper-mediated conjugate addition furnished a single diastereomer. Cued by the relative relationship reported for the appendices in the natural product, the resulting anti-adduct was elaborated into a probative target structure 1*.

Total synthesis based on the originally claimed structure of mucosin.

The first total synthesis aimed at the naturally occurring eicosanoid bicycle mucosin is reported. A practical route has been devised allowing the issues relating to the previous assignment of stereochemistry to be examined. X-ray crystallography was performed on a late stage intermediate to pinpoint the topological relationship displayed by the featured bicyclo[4.3.0]non-3-ene scaffold.

Safe Synthesis of Alkylhydroxy and Alkylamino Nitramines.

Three different protocols for the syntheses of hydroxyalkylnitramines are presented and compared. Safety issues regarding the synthesis of nitramines are also discussed.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism.

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

Ultrasound-guided pleural biopsy following a non-diagnostic thoracentesis for non-small cell lung cancer.

We report a case of a 65-year-old man with a cavitary lung mass and parietal-based pleural nodules in which a pleural ultrasound-guided approach yielded a definitive diagnosis of stage IV non-small cell lung carcinoma. Computed tomography-guided biopsy is often preferred approach for the majority of United States hospitals for sampling pleural nodules as compared to US. The advantages of an US-guided approach include [1]: increased portability [2]; decreased procedure time [3]; reduced reliance on dedicated ancillary support staff [4]; need for local anesthesia only [5]; lack of ionizing radiation exposure; and [6] cost reduction.

Prolonged Emesis Causing Esophageal Perforation: A Case Report.

Transmural esophageal rupture or Boerhaave syndrome carries a high mortality rate due to delayed diagnosis and treatment. The heterogeneity of symptoms, age, comorbidities, and the severity of illness in this group of patients add to the difficulty of the management of Boerhaave syndrome. It generally occurs in the distal part of the esophagus and may result in the leakage of gastric contents into the thoracic cavity leading to mediastinal necrosis and bacterial infection. The management relies on prompt detection and intervention with conservative care and/or surgical repair. Early recognition within 24 hours followed by primary repair of the esophagus with mediastinal and chest drainage is associated with a 90% survival rate.

Accessory Spleen Masquerading as an Intrapancreatic Tumor: A Case Report.

The finding of splenic tissue within the pancreas, also known as splenosis or intrapancreatic accessory spleen (IPAS), is a relatively uncommon condition that presents as an intrapancreatic mass. The discovery of an intrapancreatic mass often prompts a thorough diagnostic workup for a primary pancreatic malignancy, often exposing patients to unnecessary risks associated with invasive testing and even surgery. The benign, asymptomatic nature of this finding places emphasis on utilizing non-invasive techniques for confirmation of the diagnosis, reducing risks of morbidity and mortality in this patient population. Contrast-enhanced computed tomography (CT) and magnetic resonance imaging (MRI) will display near-identical signal intensities (SI) between the spleen and the intrapancreatic mass, as well as identical contrast-enhancement patterns. Nuclear medicine evaluation with Tc-99m heat-damaged red blood cells (HDRBCs) is often used as a confirmatory test and allows for differentiation from malignancies.