A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α-dependent nuclear localization signals

Nucleocytoplasmic transport regulates the passage of proteins between the nucleus and cytoplasm. In the best characterized pathway, importin (IMP) α bridges cargoes bearing basic, classical nuclear localization signals (cNLSs) to IMPβ1, which mediates transport through the nuclear pore complex. IMPα recognizes three types of cNLSs via two binding sites: the major binding site accommodates monopartite cNLSs, the minor binding site recognizes atypical cNLSs, while bipartite cNLSs simultaneously interact with both major and minor sites. Despite the growing knowledge regarding IMPα-cNLS interactions, our understanding of the evolution of cNLSs is limited. We combined bioinformatic, biochemical, functional, and structural approaches to study this phenomenon, using polyomaviruses (PyVs) large tumor antigens (LTAs) as a model. We characterized functional cNLSs from all human (H)PyV LTAs, located between the LXCXE motif and origin binding domain. Surprisingly, the prototypical SV40 monopartite NLS is not well conserved; HPyV LTA NLSs are extremely heterogenous in terms of structural organization, IMPα isoform binding, and nuclear targeting abilities, thus influencing the nuclear accumulation properties of full-length proteins. While several LTAs possess bipartite cNLSs, merkel cell PyV contains a hybrid bipartite cNLS whose upstream stretch of basic amino acids can function as an atypical cNLS, specifically binding to the IMPα minor site upon deletion of the downstream amino acids after viral integration in the host genome. Therefore, duplication of a monopartite cNLS and subsequent accumulation of point mutations, optimizing interaction with distinct IMPα binding sites, led to the evolution of bipartite and atypical NLSs binding at the minor site.

Structural and functional characterization of siadenovirus core protein VII nuclear localization demonstrates the existence of multiple nuclear transport pathways

Adenovirus protein VII (pVII) plays a crucial role in the nuclear localization of genomic DNA following viral infection and contains nuclear localization signal (NLS) sequences for the importin (IMP)-mediated nuclear import pathway. However, functional analysis of pVII in adenoviruses to date has failed to fully determine the underlying mechanisms responsible for nuclear import of pVII. Therefore, in the present study, we extended our analysis by examining the nuclear trafficking of adenovirus pVII from a non-human species, psittacine siadenovirus F (PsSiAdV). We identified a putative classical (c)NLS at pVII residues 120-128 (120PGGFKRRRL128). Fluorescence polarization and electrophoretic mobility shift assays demonstrated direct, high-affinity interaction with both IMPα2 and IMPα3 but not IMPβ. Structural analysis of the pVII-NLS/IMPα2 complex confirmed a classical interaction, with the major binding site of IMPα occupied by K124 of pVII-NLS. Quantitative confocal laser scanning microscopy showed that PsSiAdV pVII-NLS can confer IMPα/β-dependent nuclear localization to GFP. PsSiAdV pVII also localized in the nucleus when expressed in the absence of other viral proteins. Importantly, in contrast to what has been reported for HAdV pVII, PsSiAdV pVII does not localize to the nucleolus. In addition, our study demonstrated that inhibition of the IMPα/β nuclear import pathway did not prevent PsSiAdV pVII nuclear targeting, indicating the existence of alternative pathways for nuclear localization, similar to what has been previously shown for human adenovirus pVII. Further examination of other potential NLS signals, characterization of alternative nuclear import pathways, and investigation of pVII nuclear targeting across different adenovirus species is recommended to fully elucidate the role of varying nuclear import pathways in the nuclear localization of pVII.

Structural Determination of the Australian Bat Lyssavirus Nucleoprotein and Phosphoprotein Complex

Australian bat lyssavirus (ABLV) shows similar clinical symptoms as rabies, but there are currently no protein structures available for ABLV proteins. In lyssaviruses, the interaction between nucleoprotein (N) and phosphoprotein (N) in the absence of RNA generates a complex (N0P) that is crucial for viral assembly, and understanding the interface between these two proteins has the potential to provide insight into a key feature: the viral lifecycle. In this study, we used recombinant chimeric protein expression and X-ray crystallography to determine the structure of ABLV nucleoprotein bound to residues 1-40 of its phosphoprotein chaperone. Comparison of our results with the recently generated structure of RABV CVS-11 N0P demonstrated a highly conserved interface in this complex. Because the N0P interface is conserved in the lyssaviruses of phylogroup I, it is an attractive therapeutic target for multiple rabies-causing viral species.

Henipavirus Matrix Protein Employs a Non-Classical Nuclear Localization Signal Binding Mechanism

Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic species from the Henipavirus genus within the paramyxovirus family and are harbored by Pteropus Flying Fox species. Henipaviruses cause severe respiratory disease, neural symptoms, and encephalitis in various animals and humans, with human mortality rates exceeding 70% in some NiV outbreaks. The henipavirus matrix protein (M), which drives viral assembly and budding of the virion, also performs non-structural functions as a type I interferon antagonist. Interestingly, M also undergoes nuclear trafficking that mediates critical monoubiquitination for downstream cell sorting, membrane association, and budding processes. Based on the NiV and HeV M X-ray crystal structures and cell-based assays, M possesses a putative monopartite nuclear localization signal (NLS) (residues ⁸²KRKKIR⁸⁷; NLS1 HeV), positioned on an exposed flexible loop and typical of how many NLSs bind importin alpha (IMPα), and a putative bipartite NLS (²⁴⁴RR-10X-KRK²⁵⁸; NLS2 HeV), positioned within an α-helix that is far less typical. Here, we employed X-ray crystallography to determine the binding interface of these M NLSs and IMPα. The interaction of both NLS peptides with IMPα was established, with NLS1 binding the IMPα major binding site, and NLS2 binding as a non-classical NLS to the minor site. Co-immunoprecipitation (co-IP) and immunofluorescence assays (IFA) confirm the critical role of NLS2, and specifically K258. Additionally, localization studies demonstrated a supportive role for NLS1 in M nuclear localization. These studies provide additional insight into the critical mechanisms of M nucleocytoplasmic transport, the study of which can provide a greater understanding of viral pathogenesis and uncover a potential target for novel therapeutics for henipaviral diseases.

Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal

Adeno-associated viruses (AAV) are important vectors for gene therapy, and accordingly, many aspects of their cell transduction pathway have been well characterized. However, the specific mechanisms that AAV virions use to enter the host nucleus remain largely unresolved. We therefore aimed to reveal the interactions between the AAV Cap protein and the nuclear transport protein importin alpha (IMPα) at an atomic resolution. Herein we expanded upon our earlier research into the Cap nuclear localization signal (NLS) of a porcine AAV isolate, by examining the influence of upstream basic regions (BRs) towards IMPα binding. Using a high-resolution crystal structure, we identified that the IMPα binding determinants of the porcine AAV Cap comprise a bipartite NLS with an N-terminal BR binding at the minor site of IMPα, and the previously identified NLS motif binding at the major site. Quantitative assays showed a vast difference in binding affinity between the previously determined monopartite NLS, and bipartite NLS described in this study. Our results provide a detailed molecular view of the interaction between AAV capsids and the nuclear import receptor, and support the findings that AAV capsids enter the nucleus by binding the nuclear import adapter IMPα using the classical nuclear localization pathway.

Structural characterization of human importin alpha 7 in its cargo-free form at 2.5 Å resolution

Shuttling of macromolecules between nucleus and cytoplasm is a tightly regulated process mediated through specific interactions between cargo and nuclear transport proteins. In the classical nuclear import pathway, importin alpha recognizes cargo exhibiting a nuclear localization signal, and this complex is transported through the nuclear pore complex by importin beta. Humans possess seven importin alpha isoforms that can be grouped into three subfamilies, with many cargoes displaying specificity towards these importin alpha isoforms. The cargo binding sites within importin alpha isoforms are highly conserved in sequence, suggesting that specificity potentially relies on structural differences. Structures of some importin alpha isoforms, both in cargo-bound and free states, have been previously solved. However, there are currently no known structures of cargo free importin alpha isoforms within subfamily 3 (importin alpha 5, 6, 7). Here, we present the first crystal structure of human importin alpha 7 lacking the IBB domain solved at 2.5 Å resolution. The structure reveals a typical importin alpha architecture comprised of ten armadillo repeats and is most structurally conserved with importin alpha 5. Very little difference in structure was observed between the cargo-bound and free states, implying that importin alpha 7 does not undergo conformational change when binding cargo. These structural insights provide a strong platform for further evaluation of structure–function relationships and understanding how isoform specificity within the importin alpha family plays a role in nuclear transport in health and disease.

A scoping review of African swine fever virus spread between domestic and free-living pigs

Since 2007, African swine fever virus (ASFV) has spread to countries in Europe, Asia and Oceania and has caused devastating impacts on pigs and the pork industry. Transmission can be direct or indirect, and epidemiologic scenarios have been described in which spread occurs between free-living and domestic pigs. The purpose of this scoping review was to identify primary research in which authors made statements to support ASFV transmission between free-living and domestic pigs and assess the circumstances in which transmission events occurred. A search was conducted in five bibliographic databases and the grey literature. Two reviewers (from a team of ten) independently screened each record and charted data (demographics of the pig populations, their husbandry [domestic pigs] and habitat [free-living pigs], the spatial and temporal distribution of ASF, the occurrence or burden of ASF in the populations, and whether ticks were present in the geographic range of the pig populations). Data synthesis included statistics and a narrative summary. From 1,349 records screened, data were charted from 46 individual studies published from 1985 to 2020. Outbreak investigations revealed that whilst poor biosecurity of domestic pig operations was often reported, direct contact resulting in transmission between free-living and domestic pigs was rarely reported. Studies in which quantitative associations were made generally found that spread within populations was more important than spread between populations, although this was not always the case, particularly when domestic pigs were free-ranging. We conclude that there is limited evidence that transmission of ASFV between free-living and domestic pigs is an important feature of ASF epidemiology, especially in the current ASF epidemic in Europe and the Russian Federation. If ASFV elimination cannot be achieved in free-living pigs, compartmentalization of domestic pig populations from free-living populations via biosecurity strategies could be used to support trade of domestic pigs.

The Structural Features of Henipavirus Matrix Protein Driving Intracellular Trafficking

Henipaviruses are single-stranded RNA viruses that have recently emerged as zoonotic pathogens, capable of causing severe acute respiratory disease and encephalitis in humans. The prototypical henipaviruses, Hendra henipavirus and Nipah henipavirus, are a major health concern as they have high mortality rates and no currently approved human vaccine or drug therapy. Understanding the mechanisms of viral replication and pathogenicity is of critical importance for therapeutic developments. A novel target for such therapies is the Henipavirus Matrix (M) protein, a multifunctional protein that drives viral assembly and inhibits the innate immune response. These multifunctional attributes promote a complicated lifecycle: while viral replication occurs in the cytoplasm, M traffics to the nucleus, where it is ubiquitinated, for correct cellular targeting and virion packaging. In this study, we review the relationship between the structure and functions of M. In specific cases, the compatibility between structural accessibility and protein functionality is not always evident, and we highlight areas that require further investigation.

Early clinical experience of dolutegravir in an HIV cohort in a larger teaching hospital

Dolutegravir (DTG) is the third HIV integrase inhibitor (INI) available for prescription in Belfast since July 2014. It has shown high virological efficacy in both treatment-naïve and -experienced patients. We carried out a retrospective case chart analysis of HIV-1-positive adults commenced on DTG between July 2014 and September 2015. Patients were identified from records as either treatment-naïve or antiretroviral therapy (ART) experienced. Outcomes included: (1) virological response (HIV-1 RNA viral load at 0, 4, 8 and 12 weeks), (2) immunological response (CD4+ cell count at 0, 4, 8 and 12 weeks) and (3) tolerability (side effects and discontinuation). The main exclusion criteria were patients transferring care already established on DTG from other treatment centres or inadequate follow-up information (defined as attendance at <50% of clinical and serological follow-up visits). One hundred and fifty-seven commenced DTG out of 823 patients on ART; 106 (68%) were switched to DTG from another regimen, and 51 (32%) were ART-naïve. One naïve and 14 treatment-experienced patients were excluded from the analysis due to failure to attend clinical follow-up. Analysis of HIV-1 RNA viral load (HIV-1 VL) was divided into three groups: 50 new starters, 68 suppressed at switch and 24 not suppressed at switch. New starters: Baseline median HIV-1 RNA VL 71,259 copies/mL (19,536_Q25-196,413_Q75); 73% were virally undetectable (HIV-1 RNA VL <70 copies/mL) by week 4. Switching patients: Of those with an HIV-1 RNA undetectable viral load prior to switching, two were detectable with a mean viral load of 443,730 copies/mL after four weeks. Of the 24 patients detectable at switch (median HIV-1 VL 2212 [311_Q25-43,467_Q75]), 10 were detectable after four weeks. For those with a recordable viraemia, the median HIV-1 VL reduced to 376 (220_Q25-1181_Q75). At week 12, four patients were detectable with a median VL of 12,390 (567_Q25-52,285_Q75). Overall, 56 (35%) reported side effects; 40 (25%) reported either difficulty with low mood, anxiety or sleep disturbance. Sixteen (10%) discontinued DTG, with 13 (8%) due to intolerable side effects. DTG is a useful drug in naïve or switch patients. It has the potential to effectively suppress the viral load within the first four weeks of treatment and thus reduces infectiousness. Within the cohort, DTG was generally well tolerated but side effects such as low mood, anxiety and sleep disturbance were high, with 8% of patients discontinuing treatment.

Managing vaccines: defining the remit of primary care and specialist HIV clinics in the delivery of immunization to individuals with HIV infection

The British HIV Association (BHIVA) has published guidelines for immunization of HIV-infected adults. A chart review of 200 HIV-infected patients diagnosed was conducted to determine shortcomings in previous practice and determine which vaccines should routinely be given in specialist HIV clinics and which might be able to be delegated to primary care clinics. Data were collected on administration of three categories of vaccinations: (1) vaccines used in all individuals with chronic disease (pneumococcal, influenza, swine flu H1N1); (2) targeted vaccinations used in non-immune individuals with HIV who are at risk of exposure (hepatitis A and hepatitis B); (3) routine vaccines traditionally delivered to the whole population (measles/mumps/rubella [MMR], diphtheria/tetanus/pertussis and meningitis C/ACWY). Pneumococcal vaccine was delivered to 54% of eligible patients, 52% of eligible individuals completed a full hepatitis B programme of vaccination and 21% (42/200) were naturally immune; hepatitis A vaccine was delivered to 36% of eligible individuals. With increasing demands on resources, it seems likely that HIV services will have to harness resources of primary care in vaccine programmes in relation to routine vaccines. By improving communication between primary and secondary care mistakes with live vaccination decisions could be avoided; HIV services should continue to perform targeted and chronic disease vaccines, i.e. for category 1 and category 2 vaccines.

Analogy with knowledgeable learners: when analogy confers benefits and exacts costs

Though embedding analogy in a text can improve acquisition of concepts that are relatively unfamiliar to learners (Donnelly & McDaniel, 1993), it remains uncertain how analogy influences learning for learners with some background knowledge for the target material. We develop several theoretical possibilities and report an experiment to test these possibilities. Target concepts familiar to college students were expressed either in literal form or through analogy, and the concepts were presented in a manner that either facilitated or discouraged contact with subjects' prior knowledge. As revealed by multiple-choice testing, analogy facilitated learning when the targets were presented to discourage contact with prior knowledge. In contrast, analogy decreased performance when the same targets were presented to facilitate contact with prior knowledge. Possible interpretations of this unique finding are discussed.

Adulteration of soluble coffee with coffee husks and parchments

Commercial soluble coffee can be adulterated with coffee husks or parchments. Xylose is a good tracer for this type of mispractice. The analysis of total xylose in a wide selection of green beans and the assessment of its fate during processing allowed the derivation of a maximum total xylose limit of 0.40%, above which a soluble coffee should be considered as adulterated. Out of the 700 commercial soluble coffees analyzed, 81 exhibited a total xylose level above this limit. Of the samples with total xylose level lower than the limit, 99% displayed concentrations in free mannitol and total glucose below 0.30 and 2.10%, respectively.

The formation of flashbulb memories

A large group of subjects took part in a multinational test-retest study to investigate the formation of flashbulb (FB) memories for learning the news of the resignation of the British prime minister, Margaret Thatcher. Over 86% of the U.K. subjects were found to have FB memories nearly 1 year after the resignation; their memory reports were characterized by spontaneous, accurate, and full recall of event details, including minutiae. In contrast, less than 29% of the non-U.K. subjects had FB memories 1 year later; memory reports in this group were characterized by forgetting, reconstructive errors, and confabulatory responses. A causal analysis of secondary variables showed that the formation of FB memories was primarily associated with the level of importance attached to the event and level of affective response to the news. These findings lend some support to the study by R. Brown and Kulik (1977), who suggest that FB memories may constitute a class of autobiographical memories distinguished by some form of preferential encoding.

Use of analogy in learning scientific concepts

Four experiments compared learning of scientific concepts as expressed in either traditional literal form or through an analogy. Comprehension of basic-level details and inferential implications was measured through multiple-choice testing. In Experiment 1, literal or analogical renditions were presented in textual form only. In Experiment 2, text was accompanied by a dynamic video. In Experiment 3, the video and text literal rendition was compared with a text-only analogical rendition. In Experiment 4, subjects read only about a familiar domain. Subjects consistently answered basic-level questions most accurately when concepts were expressed literally, but answered inferential questions most accurately when concepts were expressed analogically. Analysis of individual differences (Experiment 2) indicated that this interaction strongly characterized the conceptual learning of science novices. The results are discussed within the framework of schema induction.

Use of analogy in learning scientific concepts

Four experiments compared learning of scientific concepts as expressed in either traditional literal form or through an analogy. Comprehension of basic-level details and inferential implications was measured through multiple-choice testing. In Experiment 1, literal or analogical renditions were presented in textual form only. In Experiment 2, text was accompanied by a dynamic video. In Experiment 3, the video and text literal rendition was compared with a text-only analogical rendition. In Experiment 4, subjects read only about a familiar domain. Subjects consistently answered basic-level questions most accurately when concepts were expressed literally, but answered inferential questions most accurately when concepts were expressed analogically. Analysis of individual differences (Experiment 2) indicated that this interaction strongly characterized the conceptual learning of science novices. The results are discussed within the framework of schema induction.

Cardiovascular adaptations to transfusion/chelation therapy of homozygote sickle cell anemia

The effect of transfusion/chelation therapy on the cardiovascular adaptations to chronic anemia in pediatric and young adult patients with homozygous sickle cell disease is uncertain. This study compares left ventricular (LV) function indexes and thoracoabdominal aortic systolic and diastolic blood flow in nontransfused and transfused patients with homozygous sickle cell disease. The study population consisted of 29 nontransfused patients with homozygous sickle cell disease, ages 0.4 to 20.9 years (group 1) and 11 chronically transfused/chelated patients, ages 4.0 to 21.8 years (group 2). The mean total hemoglobin concentration in group 2 was 28% greater than that in group 1. The mean duration of transfusion/chelation therapy in group 2 was 3.7 years. The percent of predicted LV end-diastolic and end-systolic dimensions were significantly greater than the respective controls in both groups. There was no significant difference in percent of predicted LV end-diastolic dimension (group 1, 120 +/- 12%; group 2, 120 +/- 12%) or percent of predicted LV end-systolic dimension (group 1, 120 +/- 12%; group 2, 117 +/- 8) between the groups. The percent of LV shortening fraction was similar in study groups and control subjects. Aortic systolic blood flow (cc/min/m2) for group 1 (2,426 +/- 841) and 2 (2,374 +/- 1.004) were significantly greater than corresponding control values (1,683 +/- 442, 1,736 +/- 430, respectively). Aortic diastolic blood flow was significantly greater than corresponding control values for both group 1 (699 +/- 313 vs 488 +/- 212) and group 2 (1,080 +/- 607 vs 588 +/- 219).(ABSTRACT TRUNCATED AT 250 WORDS)