Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.

Jupiter's X-Ray and UV Dark Polar Region.

We present 14 simultaneous Chandra X-ray Observatory (CXO)-Hubble Space Telescope (HST) observations of Jupiter's Northern X-ray and ultraviolet (UV) aurorae from 2016 to 2019. Despite the variety of dynamic UV and X-ray auroral structures, one region is conspicuous by its persistent absence of emission: the dark polar region (DPR). Previous HST observations have shown that very little UV emission is produced by the DPR. We find that the DPR also produces very few X-ray photons. For all 14 observations, the low level of X-ray emission from the DPR is consistent (within 2-standard deviations) with scattered solar emission and/or photons spread by Chandra's Point Spread Function from known X-ray-bright regions. We therefore conclude that for these 14 observations the DPR produced no statistically significant detectable X-ray signature.

An algorithm for the classification of mRNA patterns in eosinophilic esophagitis: Integration of machine learning.

BACKGROUND: Diagnostic evaluation of eosinophilic esophagitis (EoE) remains difficult, particularly the assessment of the patient's allergic status. OBJECTIVE: This study sought to establish an automated medical algorithm to assist in the evaluation of EoE. METHODS: Machine learning techniques were used to establish a diagnostic probability score for EoE, p(EoE), based on esophageal mRNA transcript patterns from biopsies of patients with EoE, gastroesophageal reflux disease and controls. Dimensionality reduction in the training set established weighted factors, which were confirmed by immunohistochemistry. Following weighted factor analysis, p(EoE) was determined by random forest classification. Accuracy was tested in an external test set, and predictive power was assessed with equivocal patients. Esophageal IgE production was quantified with epsilon germ line (IGHE) transcripts and correlated with serum IgE and the Th2-type mRNA profile to establish an IGHE score for tissue allergy. RESULTS: In the primary analysis, a 3-class statistical model generated a p(EoE) score based on common characteristics of the inflammatory EoE profile. A p(EoE) ≥ 25 successfully identified EoE with high accuracy (sensitivity: 90.9%, specificity: 93.2%, area under the curve: 0.985) and improved diagnosis of equivocal cases by 84.6%. The p(EoE) changed in response to therapy. A secondary analysis loop in EoE patients defined an IGHE score of ≥37.5 for a patient subpopulation with increased esophageal allergic inflammation. CONCLUSIONS: The development of intelligent data analysis from a machine learning perspective provides exciting opportunities to improve diagnostic precision and improve patient care in EoE. The p(EoE) and the IGHE score are steps toward the development of decision trees to define EoE subpopulations and, consequently, will facilitate individualized therapy.

In-season changes in heart rate recovery are inversely related to time to exhaustion but not aerobic capacity in rowers.

To determine if in-season changes in heart rate recovery (HRR) are related to aerobic fitness and performance in collegiate rowers. Twenty-two female collegiate rowers completed testing before and after their competitive season. Body fat percentage (BF%) was determined by dual-energy X-ray absorptiometry. Maximal aerobic capacity (VO2max ) and time to exhaustion (Tmax ) were determined during maximal rowing ergometer testing followed by 1 minute of recovery. HRR was expressed absolutely and as a percentage of maximal HR (HRR%1 min ). Variables were compared using paired Wilcoxon tests. Multivariable regression models were used to predict in-season changes in HRR using changes in VO2max and Tmax , while accounting for changes in BF%. From preseason to post-season, VO2max and BF% decreased (3.98±0.42 vs 3.78±0.35 L/min, P=.002 and 23.8±3.4 vs 21.3±3.9%, P<.001, respectively), while Tmax increased (11.7±1.3 vs 12.6±1.3 min, P=.002), and HRR%1 min increased (11.1±2.7 vs 13.8±3.8, P=.001). In-season changes in VO2max were not associated with HRR%1 min (P>.05). In-season changes in Tmax were related to changes in HRR%1 min (ß=-1.67, P=.006). In-season changes in BF% were not related to changes in HRR (P>.05 for all). HRR1 min and HRR%1 min were faster preseason to post-season, although the changes were unrelated to VO2max . Faster HRR%1 min post-season was inversely related to changes in Tmax . This suggests that HRR should not be used as a measure of aerobic capacity in collegiate rowers, but is a promising measure of training status in this population.

Classifying sensory profiles of children in the general population.

BACKGROUND: The aim of this study was to subtype groups of children in a community sample with and without developmental conditions, based on sensory processing patterns. METHODS: We used latent profile analysis to determine the number of sensory subtypes in a sample of n = 1132 children aged 3-14 years with typical development and developmental conditions, including autism spectrum disorder (ASD), attention-deficit hyperactivity disorder and learning disabilities. RESULTS: A five-subtype solution was found to best characterize the sample, which differed on overall degree and differential presentation of sensory processing patterns. Children with and without developmental conditions presented across subtypes, and one subtype was significantly younger in age than others (P < 0.05). CONCLUSIONS: Our results show that sensory subtypes include both children with typical development and those with developmental conditions. Sensory subtypes have previously been investigated in ASD only, and our results suggest that similar sensory subtypes are present in a sample reflective of the general population of children including those largely with typical development. Elevated scores on sensory processing patterns are not unique to ASD but rather are reflections of children's abilities to respond to environmental demands.

KOOS pain as a marker for significant knee pain two and six years after primary ACL reconstruction: a Multicenter Orthopaedic Outcomes Network (MOON) prospective longitudinal cohort study.

OBJECTIVE: The prevalence of radiographic osteoarthritis (OA) after anterior cruciate ligament reconstruction (ACLR) approaches 50%, yet the prevalence of significant knee pain is unknown. We applied three different models of Knee injury and Osteoarthritis Outcome Score (KOOS) thresholds for significant knee pain to an ACLR cohort to identify prevalence and risk factors. DESIGN: Multicenter Orthopaedic Outcomes Network (MOON) prospective cohort patients with a unilateral primary ACLR and normal contralateral knee were assessed at 2 and 6 years. Independent variables included patient demographics, validated Patient Reported Outcomes (PRO; Marx activity score, KOOS), and surgical characteristics. Models included: (1) KOOS criteria for a painful knee = quality of life subscale <87.5 and ≥2 of: KOOSpain <86.1, KOOSsymptoms <85.7, KOOSADL <86.8, or KOOSsports/rec <85.0; (2) KOOSpain subscale score ≤72 (≥2 standard deviations below population mean); (3) 10-point KOOSpain drop from 2 to 6 years. Proportional odds models (alpha ≤ 0.05) were used. RESULTS: 1761 patients of median age 23 years, median body mass index (BMI) 24.8 kg/m(2) and 56% male met inclusion, with 87% (1530/1761) and 86% (1506/1761) follow-up at 2 and 6 years, respectively. At 6 years, n = 592 (39%), n = 131 (9%) and n = 169 (12%) met criteria for models #1 through #3, respectively. The most consistent and strongest independent risk factor at both time-points was subsequent ipsilateral knee surgery. Low 2-year Marx activity score increased the odds of a painful knee at 6 years. CONCLUSIONS: Significant knee pain is prevalent after ACLR; with those who undergo subsequent ipsilateral surgery at greatest risk. The relationship between pain and structural OA warrants further study.

Meniscus treatment and age associated with narrower radiographic joint space width 2-3 years after ACL reconstruction: data from the MOON onsite cohort.

OBJECTIVE: To identify risk factors for radiographic signs of post-traumatic osteoarthritis (OA) 2-3 years after anterior cruciate ligament (ACL) reconstruction through multivariable analysis of minimum joint space width (mJSW) differences in a specially designed nested cohort. METHODS: A nested cohort within the Multicenter Orthopaedic Outcomes Network (MOON) cohort included 262 patients (148 females, average age 20) injured in sport who underwent ACL reconstruction in a previously uninjured knee, were 35 or younger, and did not have ACL revision or contralateral knee surgery. mJSW on semi-flexed radiographs was measured in the medial compartment using a validated computerized method. A multivariable generalized linear model was constructed to assess mJSW difference between the ACL reconstructed and contralateral control knees while adjusting for potential confounding factors. RESULTS: Unexpectedly, we found the mean mJSW was 0.35 mm wider in ACL reconstructed than in control knees (5.06 mm (95% CI 4.96-5.15 mm) vs 4.71 mm (95% CI 4.62-4.80 mm), P < 0.001). However, ACL reconstructed knees with meniscectomy had narrower mJSW compared to contralateral normal knees by 0.64 mm (95% C.I. 0.38-0.90 mm) (P < 0.001). Age (P < 0.001) and meniscus repair (P = 0.001) were also significantly associated with mJSW difference. CONCLUSION: Semi-flexed radiographs can detect differences in mJSW between ACL reconstructed and contralateral normal knees 2-3 years following ACL reconstruction, and the unexpected wider mJSW in ACL reconstructed knees may represent the earliest manifestation of post-traumatic osteoarthritis and warrants further study.

In situ evidence of the magnetospheric cusp of Jupiter from Juno spacecraft measurements.

The magnetospheric cusp connects the planetary magnetic field to interplanetary space, offering opportunities for charged particles to precipitate to or escape from the planet. Terrestrial cusps are typically found near noon local time, but the characteristics of the Jovian cusp are unknown. Here we show direct evidence of Jovian cusps using datasets from multiple instruments onboard Juno spacecraft. We find that the cusps of Jupiter are in the dusk sector, which is contradicting Earth-based predictions of a near-noon location. Nevertheless, the characteristics of charged particles in the Jovian cusps resemble terrestrial and Saturnian cusps, implying similar cusp microphysics exist across different planets. These results demonstrate that while the basic physical processes may operate similarly to those at Earth, Jupiter's rapid rotation and its location in the heliosphere can dramatically change the configuration of the cusp. This work provides useful insights into the fundamental consequences of star-planet interactions, highlighting how planetary environments and rotational dynamics influence magnetospheric structures.

Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes.

The discovery and mapping of cis-regulatory elements is important for understanding regulation of gene transcription in mosquito vectors of human diseases. Genome sequence data are available for 3 species, Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus (Diptera: Culicidae), representing 2 subfamilies (Culicinae and Anophelinae) that are estimated to have diverged 145 to 200 million years ago. Comparative genomics tools were used to screen genomic DNA fragments located in the 5'-end flanking regions of orthologous genes. These analyses resulted in the identification of 137 sequences, designated "mosquito motifs," 7 to 9 nucleotides in length, representing 18 families of putative cis-regulatory elements conserved significantly among the 3 species when compared to the fruit fly, Drosophila melanogaster. Forty-one of the motifs were implicated previously in experiments as sites for binding transcription factors or functioning in the regulation of mosquito gene expression. Further analyses revealed associations between specific motifs and expression profiles, particularly in those genes that show increased or decreased mRNA abundance in females following a blood meal, and those accumulating transcription products exclusively or preferentially in the midgut, fat bodies, or ovaries. These results validate the methodology and support a relationship between the discovered motifs and the conservation of hematophagy in mosquitoes.

Outcomes in patients with indeterminate pulmonary nodules undergoing resection for colorectal liver metastases.

OBJECTIVES: This study aimed to assess outcomes in patients who underwent hepatic resection for colorectal liver metastases (CRLM) with subcentimetre indeterminate pulmonary nodules (IPN) and to devise a management pathway for these patients. METHODS: Patients undergoing CRLM resection from January 2006 to December 2010 were included. Survival differences following liver resection in patients with and without IPN were determined. RESULTS: A total of 184 patients were included, 30 of whom had IPN. There were no significant differences between the IPN and non-IPN groups in terms of demographics, surgery and pathological factors. There were no significant differences between patients with and without IPN with respect to disease-free (P= 0.190) and overall (P= 0.710) survival. Fifteen patients with IPN progressed to metastatic lung disease over a median period of 10 months (range: 3-18 months); six of these patients underwent lung resection. Of the remaining 15 patients with IPN, eight showed no IPN progression and subsequent CT scans did not identify IPN in the remaining seven. CONCLUSIONS: Colorectal liver metastases patients with IPN who have resectable disease should be treated with liver resection and should be subject to intensive surveillance post-resection. Although 50% of these patients will progress to develop lung metastases, this does not appear to influence survival following liver resection.

VBNC, previously unrecognized in the life cycle of Porphyromonas gingivalis?

Bacteria are exposed to stresses during their growth and multiplication in their ecological systems to which they respond in multiple ways as expert survivalists. One such response mechanism is to convert to a viable but not culturable (VBNC) state. As the name indicates, bacteria in the VBNC state have lost their ability to grow on routine growth medium. A large number of bacteria including many pathogenic species have been reported to be able to enter a VBNC state. VBNC differs from culturable cells in various physiological properties which may result in changes in chemical resistance, adhesion, cellular morphology, metabolism, gene expression, membrane and cell wall composition and/or virulence. The ability of VBNC bacteria to return to the culturable state or resuscitate, when the stressor is removed poses a considerable threat to public health. There have been few publications that overtly describe the ability of oral pathogenic species to enter the VBNC state. However, the presence of VBNCs among oral pathogens such as Porphyromonas gingivalis in human chronic infections may be an important virulence factor and have severe implications for therapy. In this review, we intend to i) define and summarize the significance of the VBNC state in general and ii) discuss the VBNC state of oral bacteria with regard to P. gingivalis. Future studies focused on this phenomenon of intraoral VBNC would provide novel molecular insights on the virulence and persistence of oral pathogens during chronic infections and identify potential novel therapies.

Comparing Jupiter's Equatorial X-Ray Emissions With Solar X-Ray Flux Over 19 Years of the Chandra Mission.

We present a statistical study of Jupiter's disk X-ray emissions using 19 years of Chandra X-Ray Observatory (CXO) observations. Previous work has suggested that these emissions are consistent with solar X-rays elastically scattered from Jupiter's upper atmosphere. We showcase a new pulse invariant (PI) filtering method that minimizes instrumental effects which may produce unphysical trends in photon counts across the nearly two-decade span of the observations. We compare the CXO results with solar X-ray flux data from the Geostationary Operational Environmental Satellites X-ray Sensor for the wavelength band 1-8 Å (long channel), to quantify the correlation between solar activity and Jovian disk counts. We find a statistically significant Pearson's Correlation Coefficient of 0.9, which confirms that emitted Jovian disk X-rays are predominantly governed by solar activity. We also utilize the high spatial resolution of the High Resolution Camera Instrument on-board the CXO to map the disk photons to their positions on Jupiter's surface. Voronoi tessellation diagrams were constructed with the Juno Reference Model through Perijove 9 internal field model overlaid to identify any spatial preference of equatorial photons. After accounting for area and scattering across the curved surface of the planet, we find a preference of Jovian disk emission at 2-3.5 Gauss surface magnetic field strength. This suggests that a portion of the disk X-rays may be linked to processes other than solar scattering: the spatial preference associated with magnetic field strength may imply increased precipitation from the radiation belts, as previously postulated.

RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti.

BACKGROUND: Hematophagy is a common trait of insect vectors of disease. Extensive genome-wide transcriptional changes occur in mosquitoes after blood meals, and these are related to digestive and reproductive processes, among others. Studies of these changes are expected to reveal molecular targets for novel vector control and pathogen transmission-blocking strategies. The mosquito Aedes aegypti (Diptera, Culicidae), a vector of Dengue viruses, Yellow Fever Virus (YFV) and Chikungunya virus (CV), is the subject of this study to look at genome-wide changes in gene expression following a blood meal. RESULTS: Transcriptional changes that follow a blood meal in Ae. aegypti females were explored using RNA-seq technology. Over 30% of more than 18,000 investigated transcripts accumulate differentially in mosquitoes at five hours after a blood meal when compared to those fed only on sugar. Forty transcripts accumulate only in blood-fed mosquitoes. The list of regulated transcripts correlates with an enhancement of digestive activity and a suppression of environmental stimuli perception and innate immunity. The alignment of more than 65 million high-quality short reads to the Ae. aegypti reference genome permitted the refinement of the current annotation of transcript boundaries, as well as the discovery of novel transcripts, exons and splicing variants. Cis-regulatory elements (CRE) and cis-regulatory modules (CRM) enriched significantly at the 5'end flanking sequences of blood meal-regulated genes were identified. CONCLUSIONS: This study provides the first global view of the changes in transcript accumulation elicited by a blood meal in Ae. aegypti females. This information permitted the identification of classes of potentially co-regulated genes and a description of biochemical and physiological events that occur immediately after blood feeding. The data presented here serve as a basis for novel vector control and pathogen transmission-blocking strategies including those in which the vectors are modified genetically to express anti-pathogen effector molecules.

A role for endosomal proteins in alphavirus dissemination in mosquitoes.

Little is known about endosomal pathway proteins involved in arthropod-borne virus (arbovirus) assembly and cell-to-cell spread in vector mosquitoes. UNC93A and synaptic vesicle-2 (SV2) proteins are involved in intracellular transport in mammals. They show amino acid sequence conservation from mosquitoes to humans, and their transcripts are highly enriched in Aedes aegypti during arbovirus infection. Transient gene silencing of SV2 or UNC93A in mosquitoes infected with the recombinant alphavirus Sindbis MRE16-enhanced green fluorescent protein (SINV; family Togaviridae) resulted in the accumulation of viral positive- and negative-strand RNA, congregation of virus envelope antigen in intracellular networks, and reduced virus dissemination outside of the midgut. Further, UNC93A silencing, but not SV2 silencing, resulted in a 10-fold reduction in viral titres at 4 days post-infection. Together, these data support a role for UNC93A and SV2 in virus assembly or budding. Cis-regulatory elements (CREs) were identified at the 5'-ends of genes from the original data set in which SV2 and UNC93A were identified. Common CREs at the 5'-end genomic regions of a subset of enriched transcripts support the hypothesis that UNC93A transcription may be co-regulated with that of other ion transport and endosomal trafficking proteins.

Comparison of flexural properties and surface roughness of nanohybrid and microhybrid dental composites.

Recently introduced nanohybrid dental composites have promised a smoother surface finish and strength, comparable to that of microhybrid composites. This study compared the mechanical properties and surface finish of nanohybrid and microhybrid composites by measuring the flexural strength and modulus (four-point bend) and surface roughness after polishing (using atomic force microscopy) of six commercial dental composites (three nanohybrid, three microhybrid). Scanning electron microscopy (SEM) was used to qualitatively characterize filler morphology and size. The flexural strength and modulus were significantly higher among the microhybrid composites, while the nanohybrid composites exhibited significantly lower surface roughness. SEM characterization revealed differences in filler particle size and shape that could affect the flexural properties and surface roughness. Composites containing spherical filler particles exhibited higher flexural properties and lower roughness values compared to composites with irregular fillers. These results did not support the premise that nanohybrid composites offer similar mechanical properties to microhybrids in addition to a better surface finish.

Porphyromonas gingivalis W83 traffics via ICAM1 in microvascular endothelial cells and alters capillary organization in vivo.

Objective: Microvascular dysfunction is a feature of periodontal disease. P. gingivalis, one of the most common oral bacteria present in gingival tissue biofilms, has also been identified in the gingival capillaries of patients with chronic periodontitis. We sought to determine the effect of P. gingivalis W83 infection on microvascular endothelium in vivo and in vitro. Methods and Results: Interdental papillae of rats with P. gingivalis-induced alveolar bone loss had a more dilated and denser subepithelial capillary network than uninfected controls. P. gingivalis W83 was detected in the epithelial layers, the subepithelial connective tissue matrix, and subgingival capillaries. P. gingivalis invaded human dermal microvascular endothelial cells (HD-MVECS) and persisted up termination (24 h). Colocalization analysis at 2.5, 6, and 24 h post-inoculation showed that 79-88% of internalized bacteria were in ICAM-1 positive endosomes, and 10-39% were in Rab5, Rab7, or LAMP1 positive compartments, but never in autophagosomes. Antibody-based blockade of ICAM-1 significantly reduced W83 invasion in HD-MVECS. P. gingivalis infected HD-MVECS were unable to form vascular networks in Matrigel. Conclusions: P. gingivalis perturbs microvascular endothelial function and invasion of these cells via ICAM-1 may be important for microbial persistence within tissues.

Human cytomegalovirus microRNAs.

MicroRNAs (miRNAs) are approximately 22 nucleotide RNAs that mediate the posttranscriptional regulation of gene expression. miRNAs regulate diverse cellular processes such as development, differentiation, cell cycling, apoptosis, and immune responses. More than 400 miRNAs have been identified in humans and it is predicted that over 30% of human gene transcripts are regulated via miRNAs. Since 2004, many viral miRNAs have been described in several families of viruses. More than half of currently known viral miRNAs are encoded by viruses of the human Herepsviridae and 14 miRNAs have been found to be encoded by Human cytomegalovirus (HCMV). Thus far, HCMV is the only betaherpesvirus in which miRNAs have been described and these miRNAs possess many characteristics, including their genomic arrangement and temporal/spatial expression, which distinguish them from the other known herpesvirus miRNAs described. As a herpesvirus, HCMV establishes infection for the life of the host characterized by latent infection with periodic reactivation for production and spread of infectious progeny. This multifaceted life cycle of the herpesvirus requires an abundance of gene products and regulatory elements that makes cytomegalovirus genomes one of the most complex among human viruses. The defining characteristics of the cytomegalovirus and the minimal impact on genome size afforded by miRNAs inform the logic of virus-encoded miRNAs.

Autophagy and related mechanisms of lysosome-mediated protein degradation.

Lysosomes play a central role in the degradation of extracellular and intracellular macromolecules. These organelles contain hydrolytic enzymes capable of degrading proteins, proteoglycans, nucleic acids, and lipids. The mechanisms involved in the delivery of such intracellular compounds to the lysosome have been characterized in several recent studies. The sequestration of intracellular macromolecules for intralysosomal degradation can occur by crinophagy, hsc73-mediated carrier transport, or autophagy. The major route of delivery of cellular proteins and RNA into lysosomes is by autophagy. Furthermore, autophagy is regulated by nutrients and hormones, thus allowing the cell to adjust its degradative state to environmental changes.

Studies on the mechanisms of autophagy: maturation of the autophagic vacuole.

Data presented in the accompanying paper suggests nascent autophagic vacuoles are formed from RER (Dunn, W. A. 1990. J. Cell Biol. 110:1923-1933). In the present report, the maturation of newly formed or nascent autophagic vacuoles into degradative vacuoles was examined using morphological and biochemical methods combined with immunological probes. Within 15 min of formation, autophagic vacuoles acquired acid hydrolases and lysosomal membrane proteins, thus becoming degradative vacuoles. A previously undescribed type of autophagic vacuole was also identified having characteristics of both nascent and degradative vacuoles, but was different from lysosomes. This intermediate compartment contained only small amounts of cathepsin L in comparison to lysosomes and was bound by a double membrane, typical of nascent vacuoles. However, unlike nascent vacuoles vet comparable to degradative vacuoles, these vacuoles were acidic and contained the lysosomal membrane protein, lgp120, at the outer limiting membrane. The results were consistent with the stepwise acquisition of lysosomal membrane proteins and hydrolases. The presence of mannose-6-phosphate receptor in autophagic vacuoles suggested a possible role of this receptor in the delivery of newly synthesized hydrolases from the Golgi apparatus. However, tunicamycin had no significant effect on the amount of mature acid hydrolases present in a preparation of autophagic vacuoles isolated from a metrizamide gradient. Combined, the results suggested nascent autophagic vacuoles mature into degradative vacuoles in a stepwise fashion: (a) acquisition of lysosomal membrane proteins by fusing with a vesicle deficient in hydrolytic enzymes (e.g., prelysosome); (b) vacuole acidification; and (c) acquisition of hydrolases by fusing with preexisting lysosomes or Golgi apparatus-derived vesicles.

Studies on the mechanisms of autophagy: formation of the autophagic vacuole.

Autophagic vacuoles form within 15 min of perfusing a liver with amino acid-depleted medium. These vacuoles are bound by a "smooth" double membrane and do not contain acid phosphatase activity. In an attempt to identify the membrane source of these vacuoles, I have used morphological techniques combined with immunological probes to localize specific membrane antigens to the limiting membranes of newly formed or nascent autophagic vacuoles. Antibodies to three integral membrane proteins of the plasma membrane (CE9, HA4, and epidermal growth factor receptor) and one of the Golgi apparatus (sialyltransferase) did not label these vacuoles. Internalized epidermal growth factor and its membrane receptor were not found in nascent autophagic vacuoles but were present in lysosome-like degradative autophagic vacuoles. All these results suggested that autophagic vacuoles were not formed from plasma membrane, Golgi apparatus, or endosome constituents. Antisera prepared against integral membrane proteins (14, 25, and 40 kD) of the RER was found to label the inner and outer limiting membranes of almost all nascent autophagic vacuoles. In addition, ribophorin II was identified at the limiting membranes of many nascent autophagic vacuoles. Finally, secretory proteins, rat serum albumin and alpha 2u-globulin, were localized to the lumen of the RER and to the intramembrane space between the inner and outer membranes of some of these vacuoles. The results were consistent with the formation of autophagic vacuoles from ribosome-free regions of the RER.