bluuebunny/crossref_metadata_2025_split huggingface dataset:
Daily Engine Performance Trending Using Common Flight Regime Identification
Authors: Mallamo Declan P. , Azarian Michael H. , Pecht Michael G. 
Published: October 2024

Abstract
Accurate flight regime identification is critical for enhancing aircraft efficiency and safety. Traditionally, predictive models for aircraft operation have relied on complex, black-box machine learning techniques that lack transparency. This study introduces a more interpretable approach by leveraging the New Comprehensive Modular Aero-Propulsion System Simulation (N-CMAPSS) dataset and combining expanding window classification, voting schemes, and spectral clustering to detect distinct flight regimes. The method applies elastic registration to align time-shifted patterns and functional principal component analysis (FPCA) to reduce dimensionality, capturing core dynamics across flight regimes. These transformed features are fed into a genetic algorithm (GA)-assisted orthogonal matching pursuit (OMP) for sparse feature selection. Through evolutionary selection, crossover, and mutation, the most informative features are identified, enabling accurate predictions while maintaining transparency. This method outperforms more complex models in certain test cases, offering a balance between accuracy and interpretability that is essential for predictive maintenance and safety applications.
Transiently boosting Vγ9+Vδ2+ γδ T cells early in Mtb coinfection of SIV-infected juvenile macaques does not improve Mtb host resistance
Authors: Larson Erica C. , Ellis Amy L. , Rodgers Mark A. , Gubernat Abigail K. , Gleim Janelle L. , Moriarty Ryan V. , Balgeman Alexis J. , de Menezes Yonne T. , Ameel Cassaundra L. , Fillmore Daniel J. , Pergalske Skyler M. , Juno Jennifer A. , Maiello Pauline , Chishti Harris B. , Lin Philana Ling , Godfrey Dale I. , Kent Stephen J. , Pellicci Daniel G. , Ndhlovu Lishomwa C. , O'Connor Shelby L. , Scanga Charles A. 
Published: October 2024

ABSTRACT

Children living with HIV have a higher risk of developing tuberculosis (TB), a disease caused by the bacterium
Mycobacterium tuberculosis
(Mtb). Gamma delta (γδ) T cells in the context of HIV/Mtb coinfection have been understudied in children despite
in vitro
evidence suggesting γδ T cells assist with Mtb control. We investigated whether boosting a specific subset of γδ T cells, phosphoantigen-reactive Vγ9+Vδ2+ cells, could improve TB outcome using a nonhuman primate model of pediatric HIV/Mtb coinfection. Juvenile Mauritian cynomolgus macaques (MCM), equivalent to 4- to 8-year-old children, were infected intravenously (i.v.) with SIV. After 6 months, MCM were coinfected with a low dose of Mtb and then randomized to receive zoledronate (ZOL), a drug that increases phosphoantigen levels, (
n
= 5; i.v.) at 3 and 17 days after Mtb accompanied by recombinant human IL-2 (s.c.) for 5 days following each ZOL injection. A similarly coinfected MCM group (
n
= 5) was injected with saline as a control. Vγ9+Vδ2+ γδ T cell frequencies spiked in the blood, but not airways, of ZOL+IL-2-treated MCM following the first dose, however, were refractory to the second dose. At necropsy 8 weeks after Mtb, ZOL+IL-2 treatment did not reduce pathology or bacterial burden. γδ T cell subset frequencies in granulomas did not differ between treatment groups. These data show that transiently boosting peripheral γδ T cells with ZOL+IL-2 soon after Mtb coinfection of SIV-infected MCM did not improve Mtb host defense.
Stimulation of neutral lipid synthesis via viral growth factor signaling and ATP citrate lyase during vaccinia virus infection
Authors: Pant Anil , Brahim Belhaouari Djamal , Dsouza Lara , Yang Zhilong 
Published: October 2024

ABSTRACT

Fatty acid metabolism can provide various products essential for viral infections. How vaccinia virus (VACV), the prototype of poxviruses, modulates fatty acid metabolism is not well understood. Here, we show that VACV infection results in increased neutral lipid droplet synthesis, the organelles that play a crucial role in storing and mobilizing fatty acids for energy production via β-oxidation. Citrate is the first tricarboxylic acid (TCA) cycle intermediate that can be transported to the cytosol to be converted to acetyl-CoA for
de novo
fatty acid biosynthesis. We found that VACV infection stimulates the S455 phosphorylation of ATP citrate lyase (ACLY), a pivotal enzyme that links citrate metabolism with lipid metabolism. We demonstrate that the inhibition of neutral lipid droplet synthesis and ACLY severely suppresses VACV replication. Remarkably, we found that virus growth factor (VGF)-induced signaling is essential for the VACV-mediated upregulation of ACLY phosphorylation and neutral lipid droplets. Finally, we report that VGF-induced EGFR-Akt pathway and ACLY phosphorylation are important for VACV stimulation of neutral lipid synthesis. These findings identified a new way of rewiring cell metabolism by a virus and a novel function for VGF in the governance of virus-host interactions through the induction of a key enzyme at the crossroads of the TCA cycle and fatty acid metabolism. Our study also provides a mechanism for the role played by VGF and its downstream signaling cascades in the modulation of lipid metabolism in VACV-infected cells.

IMPORTANCE
Neutral lipid droplets are vital players in cellular metabolism. Here, we showed that VACV induces neutral lipid droplet synthesis in infected primary human foreskin fibroblasts and identified the cellular and viral factors needed. We identified VACV encoded growth factor (VGF) as an essential viral factor that induces cellular EGFR-Akt signaling to increase lipid droplets. Interestingly, VACV increases the S455 phosphorylation of ACLY, a key metabolic enzyme that sits at the crossroads of carbohydrate and lipid metabolism in a VGF-EGFR-Akt-dependent manner. We also found that ACLY is vital for VACV-induced lipid droplet synthesis. Our findings identified the modulation of ACLY by a virus and identified it as a potential target for antiviral development against pathogenic poxviruses. Our study also expands the role of growth factor signaling in boosting VACV replication by targeting fatty acid metabolism.
Activity and cryo-EM structure of the polymerase domain of the human norovirus ProPol precursor
Authors: McSweeney Alice M. , Eruera Alice-Roza , McKenzie-Goldsmith Geena M. , Bouwer James C. , Brown Simon H. J. , Stubbing Louise A. , Hubert Jonathan G. , Shrestha Rinu , Sparrow Kevin J. , Brimble Margaret A. , Harris Lawrence D. , Evans Gary B. , Bostina Mihnea , Krause Kurt L. , Ward Vernon K. 
Published: October 2024

ABSTRACT

Human norovirus (HuNV) is a leading cause of acute gastroenteritis worldwide with most infections caused by genogroup I and genogroup II (GII) viruses. Replication of HuNV generates both precursor and mature proteins during processing of the viral polyprotein that are essential to the viral lifecycle. One such precursor is protease-polymerase (ProPol), a multi-functional enzyme comprised of the norovirus protease and polymerase proteins. This work investigated HuNV ProPol by determining the
de novo
polymerase activity, protein structure, and antiviral inhibition profile. The GII ProPol
de novo
enzymatic efficiencies (
k
cat
/
K
m
) for RNA templates and ribonucleotides were equal or superior to those of mature GII Pol on all templates measured. Furthermore, GII ProPol was the only enzyme form active on a poly(A) template. The first structure of the polymerase domain of HuNV ProPol in the unliganded state was determined by cryo-electron microscopy at a resolution of 2.6 Å. The active site and overall architecture of ProPol are similar to those of mature Pol. In addition, both galidesivir triphosphate and PPNDS inhibited polymerase activity of GII ProPol, with respective half-maximal inhibitory concentration (IC
50
) values of 247.5 µM and 3.8 µM. In both instances, the IC
50
obtained with ProPol was greater than that of mature Pol, indicating that ProPol can exhibit different responses to antivirals. This study provides evidence that HuNV ProPol possesses overlapping and unique enzyme properties compared with mature Pol and will aid our understanding of the replication cycle of the virus.

IMPORTANCE
Despite human norovirus (HuNV) being a leading cause of acute gastroenteritis, the molecular mechanisms surrounding replication are not well understood. Reports have shown that HuNV replication generates precursor proteins from the viral polyprotein, one of which is the protease-polymerase (ProPol). This precursor is important for viral replication; however, the polymerase activity and structural differences between the precursor and mature forms of the polymerase remain to be determined. We show that substrate specificity and polymerase activity of ProPol overlap with, but is distinct from, the mature polymerase. We employ cryo-electron microscopy to resolve the first structure of the polymerase domain of ProPol. This shows a polymerase architecture similar to mature Pol, indicating that the interaction of the precursor with substrates likely defines its activity. We also show that ProPol responds differently to antivirals than mature polymerase. Altogether, these findings enhance our understanding of the function of the important norovirus ProPol precursor.
IFI27 inhibits HIV-1 replication by degrading Gag protein through the ubiquitin-proteasome pathway
Authors: He Wen-Qiang , Pang Wei , Li Na , Li An-Qi , Li Yi-Hui , Lu Ying , Shen Fan , Xin Rong , Song Tian-Zhang , Tian Ren-Rong , Yang Liu-Meng , Zheng Yong-Tang 
Published: October 2024

ABSTRACT

Type I interferon (IFN-I) and its downstream genes play a profound role in HIV infection. In this study, we found that an IFN-inducible gene, IFI27, was upregulated in HIV-1 infection, which in turn efficiently suppressed HIV-1 replication, specially degraded the viral gag protein, including p24 and p55 subunits. Notably, the anti-HIV-1 activity of IFI27 in Old World monkeys surpassed that in New World monkeys, and IFI27 has a higher potentially inhibitory effect on HIV-1 than simian immunodeficiency virus (SIV). Our initial observations showed that NPM-IFI27, the IFI27 variant in northern pig-tailed macaque (
Macaca leonina
, NPM), exhibited a strong anti-HIV-1 activity. Further investigation demonstrated that NPM-IFI27 degraded p24 and p55 via the ubiquitin-proteasome pathway, with NPM-IFI27-37–115 interacting with the p24-N domain, and the NPM-IFI27-76–122 domain was closely associated with K48 ubiquitin recruitment. Additionally, Skp2 was identified as the probable E3 ubiquitin ligase responsible for the degradation of p24 and p55. Similarly, human IFI27 (Hu-IFI27) showed a mechanism similar to NPM-IFI27 in HIV-1 inhibition. These findings underscore the pivotal role of NPM-IFI27 in HIV-1 infection and provide a potential strategy for clinical anti-HIV-1 therapy.

IMPORTANCE
HIV-1 infection can trigger the production of IFN-I, which subsequently activates the expression of various IFN-stimulated genes (ISGs) to antagonize the virus. Therefore, discovering novel host antiviral agents for HIV-1 treatment is crucial. Our previous study revealed that IFI27 can influence HIV-1 replication. In this study, we observed that the NPM-IFI27 complex specifically inhibited HIV-1 by targeting its Gag protein. Further exploration demonstrated that IFI27 interacted with the HIV-1 p24 and p55 proteins, leading to their degradation through the ubiquitin-proteasome pathway. Notably, the NPM-IFI27-37–122 variant exhibited potent anti-HIV-1 activity, comparable to that of SAMHD1. These findings highlight the critical role and inhibitory mechanism of NPM-IFI27 in HIV-1 infection, providing a potential strategy for clinical antiviral therapy.
Electron tomography visualization of HIV-1 virions trapped by fusion inhibitors to host cells in infected tissues
Authors: Ladinsky Mark S. , Zhu Li , Ullah Irfan , Uchil Pradeep D. , Kumar Priti , Kay Michael S. , Bjorkman Pamela J. 
Published: October 2024

ABSTRACT

HIV-1 delivers its genetic material to infect a cell after fusion of the viral and host cell membranes, which takes place after the viral envelope (Env) binds host receptor and co-receptor proteins. Binding of host receptor CD4 to Env results in conformational changes that allow interaction with a host co-receptor (CCR5 or CXCR4). Further conformational rearrangements result in an elongated pre-hairpin intermediate structure in which Env is anchored to the viral membrane by its transmembrane region and to the host cell membrane by its fusion peptide. Although budding virions can be readily imaged by electron tomography (ET) of HIV-1-infected tissues and cultured cells, virions that are fusing (attached to host cells via pre-hairpin intermediates) are not normally visualized, perhaps because the process of membrane fusion is too fast to capture by ET. To image virions during fusion, we used fusion inhibitors to prevent downstream conformational changes in Env that lead to membrane fusion, thereby trapping HIV-1 virions linked to target cells by pre-hairpin intermediates. ET of HIV-1 pseudovirions bound to CD4
+
/CCR5
+
TZM-bl cells revealed presumptive pre-hairpin intermediates as 2–4 narrow spokes linking a virion to the cell surface. To extend these results to a more physiological setting, we used ET to image tissues and organs derived from humanized bone marrow/liver/thymus mice infected with HIV-1 and then treated with CPT31, a high-affinity D-peptide fusion inhibitor linked to cholesterol. Trapped HIV-1 virions were found in all tissues studied (small intestine, mesenteric lymph nodes, spleen, and bone marrow), and spokes representing pre-hairpin intermediates linking trapped virions to cell surfaces were similar in structure and number to those seen in the previous pseudovirus and cultured cell ET study.

IMPORTANCE
Trapped and untrapped HIV-1 virions, both mature and immature, were distinguished by localizing spokes via 3D tomographic reconstructions of HIV-1 infected and fusion-inhibitor-treated tissues of humanized mice. The findings of trapped HIV-1 virions in all tissues examined demonstrate a wide distribution of the CPT31 inhibitor, a desirable property for a potential therapeutic. In addition, the presence of virions trapped by spokes, particularly in vascular endothelial cells, demonstrates that the fusion inhibitors can be used as markers for potential HIV-1-target cells within tissues, facilitating the mapping of HIV-1 target cells within the complex cellular milieu of infected tissues.
Adeno-associated virus 9 (AAV9) viral proteins VP1, VP2, and membrane-associated accessory protein (MAAP) differentially influence
in vivo
transgene expression
Authors: Powell Sara K. , McCown Thomas J. 
Published: October 2024

ABSTRACT

Adeno-associated virus (AAV) is a
Dependoparvovirus
with a ssDNA ~4.7 kb genome in a ~25 nm icosahedral capsid structure. AAV genomes encode nine known functional proteins from two open reading frames between two inverted terminal repeats (ITRs). In recombinant AAV vectors for gene therapy use, the AAV genome is replaced with a transgene of interest flanked by ITRs and subsequently packaged within an AAV capsid made up of three viral structural proteins (VP1, VP2, and VP3) in an approximate 1:1:10 ratio, respectively. The AAV capsid, particularly VP3, has traditionally been ascribed to capsid-cellular receptor binding. However, AAV9 VP1/VP2 exhibits a capsid-promoter interaction that can alter neuronal cellular tropism in the rat and non-human primate central nervous system. This capsid-promoter interaction is altered by AAV9EU (AAV9 with six glutamates inserted at aa139) which exhibits a significant reduction in nuclear transgene DNA, a decrease in neuronal transduction, and a reduction
in vivo
relative transgene mRNA levels. AAV9EU has six amino acid insertions in VP1, VP2, and MAAP (membrane-associated accessory protein), but no combination of VP with MAAP recapitulated the AAV9EU
in vivo
phenotype. Surprisingly, AAV9 produced in the absence of MAAP9 exhibits an increase in relative transgene levels. While co-infusing two AAV9 vectors, differing only in transgene and MAAP9 presence during production, exhibit a significantly increased
in vivo
transgene fluorescence intensity by fivefold of both transgenes. Together, an MAAP9-related activity acts both in
cis
and in
trans
to increase AAV9 transgene mRNA levels and AAV9 transgene protein levels
in vivo
.

IMPORTANCE

Recombinant adeno-associated viruses (AAVs) are used extensively in clinical gene therapy for treating a range of tissues and pathologies in humans. In particular, AAV9 occupies a prominent position in central nervous system (CNS) gene therapy given its central role in ongoing clinical trials and an FDA-approved therapeutic. Despite its widespread use, recent studies have identified unique roles for the AAV capsid in
in vivo
transgene expression; for example, interior-facing capsid residues of AAV VP1 and VP2 modulate cellular transgene expression
in vivo
. The following experiments identified that the AAV9 MAAP protein exerts a significant influence on
in vivo
transgene expression. This finding could further explain how AAV can remain latent after infection
in vivo
. Together, these studies provide novel functional insights that highlight the importance of further understanding basic AAV biology.
Genetic variation in individuals from a population of the minimalist bacteriophage Merri-merri-uth nyilam marra-natj driving evolution of the virus
Authors: Thung Tze Y. , Hall Alex , Jati Afif P. , White Murray E. , Bamert Rebecca S. , Tan Kher Shing , Press Cara , Taiaroa George , Short Francesca L. , Dunstan Rhys A. , Lithgow Trevor 
Published: October 2024

ABSTRACT

In a survey of a waterway on Wurundjeri land, two sub-populations of the bacteriophage Merri-merri-uth nyilam marra-natj (phage MMNM) were isolated on a permissive host,
Klebsiella
B5055 of capsule-type K2, but were distinguished by minor phenotypic differences. The variant phage MMNM(Ala
134
) showed an inhibited activity against
Klebsiella
AJ174-2, and this was used as a basis to select for further variation through experimental evolution. Over the course of an evolution experiment, 20 phages that evolved distinct phenotypes in terms of the morphologies of plaques formed when they infected host
Klebsiella
were subject to whole-genome sequencing. The evolved phages had mutations in a small set of proteins that contribute to the baseplate portion of the phage virion. Phages MMNM and MMNM(Ala
134
) are minimalist phages, with baseplates formed from only five predicted subunits, akin to other minimalist phages Pam3 and XM1. The homology between all three minimalist phages provided a structural framework to interpret the two classes of mutations derived through evolution in the presence of the semi-permissive host: those that affect the interfacial surfaces between baseplate subunits, and those in a base-plate associated tail-fiber. This study evidences that multiple small mutations can be fixed into a sub-population of phage to provide a basis for phenotypic variation that we suggest could ultimately provide for a shift of virus properties, as an alternative evolutionary scenario to the major genetic events that result in more well-studied evolutionary mechanism of phage mosaicism.

IMPORTANCE

Bacteriophages (phages) are viruses that prey on bacteria. This study sampled natural phage populations to test the hypothesis that untapped genetic variation within a population can be the basis for the selection of phages to diversify their host-range. Sampling of a freshwater site revealed two populations of the phage Merri-merri-uth nyilam marra-natj (phage MMNM), differing by a variant residue (Val134Ala) in the baseplate protein MMNM_26. This sequence variation modulated bacterial killing in plaques, and further evolution of the phages on a semi-permissive bacterial host led to a new generation of phages with more diverse phenotypes in killing the bacterium
Klebsiella pneumoniae
.
A novel antibody treatment reduces deformed wing virus loads in the western honey bee (
Apis mellifera
)
Authors: MacMillan N. J. J. , Hause B. M. , Nordseth T. , Felden A. , Baty J. W. , Pitman J. L. , Lester P. J. 
Published: October 2024

ABSTRACT

The deformed wing virus (
Iflavirus aladeformis
) (DWV) is a key driver of colony loss in the western honey bee (
Apis mellifera
). Here, we demonstrate that orally delivered anti-DWV antibodies can act systemically to reduce DWV loads in naturally infected honey bees. Immunoglobulin Y (IgY) was produced in adult chickens against two DWV proteins, harvested from their eggs, and fed to bees in a sucrose solution. An enzyme-linked immunosorbent assay demonstrated that orally delivered anti-DWV IgY migrated to the hemolymph. We next assessed the ability of orally delivered anti-DWV IgY to reduce DWV viral loads in naturally infected bees using qPCR. An antibody treatment resulted in a significant eightfold viral load reduction in DWV-infected bees. Our findings demonstrate the potential for antibody treatments to help mitigate the losses attributed to DWV in
A. mellifera
.

IMPORTANCE

Deformed wing virus (DWV) is considered to be a key component of declining honey bee health which threatens global food production. The virus can result in significantly shortened lifespan, deformities in developing bees, and impaired cognition. There is currently no method to directly control the virus. The virus can be indirectly controlled with acaricidal treatments that target a key vector, the parasitic varroa mite (
Varroa destructor
). But acaricide resistance and a lack of effective alternatives for the control of both Varroa and DWV are major threats to beekeeping and the wider agricultural industry. Our research presents a significant development in the ability to reduce DWV burden in honey bees using IgY antibodies. Moreover, immunoglobulin Y has the potential to be more broadly established as a new treatment modality to combat other pathogens and parasites in
A. mellifera.