bluuebunny/crossref_metadata_2025 huggingface dataset:
Caspase-2 kills cells with extra centrosomes
Authors: Rizzotto Dario , Vigorito Vincenza , Rieder Patricia , Gallob Filip , Moretta Gian Mario , Soratroi Claudia , Riley Joel S. , Bellutti Florian , Veli Stefano Li , Mattivi Alessia , Lohmüller Michael , Herzog Sebastian , Bornhauser Beat C. , Jacotot Etienne D. , Villunger Andreas , Fava Luca L.
Published: October 2024

Centrosomes are membrane-less organelles that orchestrate a wide array of biological functions by acting as microtubule organizing centers. Here, we report that caspase-2–driven apoptosis is elicited in blood cells failing cytokinesis and that extra centrosomes are necessary to trigger this cell death. Activation of caspase-2 depends on the PIDDosome multi-protein complex, and priming of PIDD1 at extra centrosomes is necessary for pathway activation. Accordingly, loss of its centrosomal adapter, ANKRD26, allows for cell survival and unrestricted polyploidization in response to cytokinesis failure. Mechanistically, cell death is initiated upstream of mitochondria via caspase-2–mediated processing of the BCL2 family protein BID, driving BAX/BAK-dependent mitochondrial outer membrane permeabilization (MOMP). Remarkably, BID-deficient cells enforce apoptosis by engaging p53-dependent proapoptotic transcriptional responses initiated by caspase-2. Consistently, BID and MDM2 act as shared caspase-2 substrates, with BID being kinetically favored. Our findings document that the centrosome limits its own unscheduled duplication by the induction of PIDDosome-driven mitochondrial apoptosis to avoid potentially pathogenic polyploidization events.
Defensive polyketides produced by an abundant gastropod are candidate keystone molecules in estuarine ecology
Authors: Scesa Paul , Nguyen Helen , Weiss Paige , Rodriguez Alejandra P. , Garchow Matthew , Ohlemacher Shannon I. , Prappas Evangelia , Caplins Serena A. , Bewley Carole A. , Bohnert Laine , Zellmer Amanda J. , Wood Eric M. , Schmidt Eric W. , Krug Patrick J.
Published: October 2024

Secondary metabolites often function as antipredator defenses, but when bioactive at low concentrations, their off-target effects on other organisms may be overlooked. Candidate “keystone molecules” are proposed to affect community structure and ecosystem functions, generally originating as defenses of primary producers; the broader effects of animal chemistry remain largely unexplored, however. Here, we characterize five previously unreported polyketides (alderenes A to E) biosynthesized by sea slugs reaching exceptional densities (up to 9000 slugs per square meter) in Northern Hemisphere estuaries. Alderenes comprise only 0.1% of slug wet weight, yet rendered live slugs or dead flesh unpalatable to three co-occurring consumers, making a potential food resource unavailable and redirecting energy flow in critical nursery habitat. Alderenes also displaced infauna from the upper sediment of the mudflat but attracted ovipositing snails. By altering communities, such compounds may have unexpected cascading effects on processes ranging from bioturbation to reproduction of species not obviously connected to the producing organisms, warranting greater attention by ecologists.
Stereoselective synthesis of geminal bromofluoroalkenes by kinetically controlled selective conversion of oxaphosphetane intermediates
Authors: Jin Jaeseong , Song Su-min , Choi Jun-Ho , Chung Won-jin
Published: October 2024

Geminal bromofluoroalkenes are an important subclass of versatile organic interhalide, which can serve as useful synthetic precursors to monofluoroalkenes that are valuable amide group isosteres. Nonetheless, despite the vast advancement of olefination methodologies, the broadly applicable stereoselective synthesis remained elusive for geminal bromofluoroalkenes before our work. In particular, the seemingly straightforward Wittig-type approach with interhalogenated phosphorus ylide has been unsuccessful because of the difficulty in the diastereoselective oxaphosphetane formation. Here, we describe a conceptually distinctive strategy, by which the stereoselectivity is gained via the selective decomposition of the oxaphosphetane intermediates. The suitably identified phosphorus(III) reagent and reaction medium enabled efficient kinetic differentiation, which was supported by nuclear magnetic resonance analysis and density functional theory calculation. Through our method, the highly diastereoselective synthesis of geminal
E
-bromofluoroalkenes was accomplished in one step. Furthermore, the generality was demonstrated by accommodating a wide range of readily available carbonyl compounds, including ketones and pharmaceutical substrates.
Understanding the sense of self through robotics
Authors: Prescott Tony J. , Vogeley Kai , Wykowska Agnieszka
Published: October 2024

Robotics can play a useful role in the scientific understanding of the sense of self, both through the construction of embodied models of the self and through the use of robots as experimental probes to explore the human self. In both cases, the embodiment of the robot allows us to devise and test hypotheses about the nature of the self, with regard to its development, its manifestation in behavior, and the diversity of selves in humans, animals, and, potentially, machines. This paper reviews robotics research that addresses the topic of the self—the minimal self, the extended self, and disorders of the self—and highlights future directions and open challenges in understanding the self through constructing its components in artificial systems. An emerging view is that key phenomena of the self can be generated in robots with suitably configured sensor and actuator systems and a layered cognitive architecture involving networks of predictive models.
Inhibition of an Alzheimer’s disease–associated form of necroptosis rescues neuronal death in mouse models
Authors: Koper Marta J. , Moonen Sebastiaan , Ronisz Alicja , Ospitalieri Simona , Callaerts-Vegh Zsuzsanna , T’Syen Dries , Rabe Sabine , Staufenbiel Matthias , De Strooper Bart , Balusu Sriram , Thal Dietmar Rudolf
Published: October 2024

Necroptosis is a regulated form of cell death that has been observed in Alzheimer’s disease (AD) along with the classical pathological hallmark lesions of amyloid plaques and Tau neurofibrillary tangles. To understand the neurodegenerative process in AD, we studied the role of necroptosis in mouse models and primary mouse neurons. Using immunohistochemistry, we demonstrated activated necroptosis-related proteins in transgenic mice developing Tau pathology and in primary neurons from amyloid precursor protein (APP)–Tau double transgenic mice treated with phosphorylated Tau seeds derived from a patient with AD but not in APP transgenic mice that only exhibited β-amyloid deposits. Necroptosis proteins in granulovacuolar degeneration (GVD) bodies were associated with neuronal loss in mouse brain regions also known to be vulnerable to GVD in the human AD brain. Necroptosis inhibitors lowered the percentage of neurons showing GVD and reduced neuronal loss, both in transgenic mice and in primary mouse neurons. This suggests that a GVD-associated form of necroptosis that we refer to as “GVD-necroptosis” may represent a delayed form of necroptosis in AD. We propose that inhibition of necroptosis could rescue this type of neuronal death in AD.
Bayesian modeling for analyzing heterogeneous response in preclinical mouse tumor models
Authors: Zhang Bairu , Magiera Lukasz , Candido Juliana , Muraeva Olga , Coates Ulrichsen Jane , Eyles Jim , Galvani Elena , Karp Natasha A.
Published: October 2024

In anticancer research, tumor growth measured in mouse models is important for assessing treatment efficacy for a treatment to progress to human clinical trials. Statistical analysis of time-to-event tumor volume data is complex because of heterogeneity in response and welfare-related data loss. Traditional statistical methods of testing the mean difference between groups are not robust because they assume common responses across a population. Heterogeneity in response is also seen in the clinic, and consequently, the assessment of the treatment considers the diversity through classification of the individual’s response using the RECIST (Response Evaluation Criteria in Solid Tumors). To provide a comparable and translatable assessment of in vivo tumor response, we developed a statistical method called INSPECT (IN vivo reSPonsE Classification of Tumors) for analyzing heterogeneous responses through Bayesian modeling. This method can classify individual tumor behaviors into the categories of nonresponder, modest responder, stable responder, and regressing responder. Using both published and simulated data, we show that INSPECT methodology is more accurate and sensitive than existing methods with respect to balancing false-negative and false-positive rates. A case study demonstrates the value of INSPECT in drug projects for supporting the translation of drug efficacy from the preclinical phase into clinical trials. We also provide a package, “INSPECTumours,” that launches a web interface to enable users to conduct the analysis and generate reports.
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

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

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

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

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

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

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

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

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.
Cell aggregation mediated by
ACE2
deletion in
Candida auris
modulates fungal colonization and host immune responses in the skin
Authors: Balakumar Abishek , Cox Abigail , Thangamani Shankar
Published: October 2024

Candida auris
is an emerging multi-drug-resistant fungal pathogen that colonizes the skin and causes invasive infections in hospitalized patients. Multi-cellular aggregative phenotype is widely reported in the
C. auris
isolates, but its role in skin colonization and host immune response is not yet known. In this study, we generated aggregative phenotype by deleting the
ACE2
gene in
C. auris
and determined the fungal colonization and host immune response using an intradermal mouse model of
C. auris
skin infection. Our results indicate that mice infected with
ace2
Δ strain had significantly lower fungal load after 3 and 14 days post-infections compared to the non-aggregative wild-type and the
ACE2
reintegrated strain. The colonization of
ace2
Δ is associated with increased recruitment of CD11b
+
Ly6G
+
neutrophils and decreased accumulation of CD11b
+
Ly6 C
hi
inflammatory monocytes and CD11b
+
MHCII
+
CD64
+
macrophages. Furthermore, Th17 cells and type 3 innate lymphoid cells (ILCs) were significantly increased in the skin tissue of
ace2
Δ infected mice. Our findings suggest that aggregative phenotype mediated by
ACE2
deletion in
C. auris
induces potent neutrophil and IL-17-mediated immune response and reduces fungal colonization in the skin.

IMPORTANCE

C. auris
is a rapidly emerging fungal pathogen that can colonize hospitalized patients, especially in skin tissue, and cause invasive infections.
C. auris
isolates exhibit morphological heterogeneity, and the multicellular aggregative phenotype of
C. auris
is reported frequently in clinical settings. Understanding the role of fungal morphotypes in colonization, persistence, and immune response in the skin microenvironment will have potential applications in clinical diagnosis and novel preventive and therapeutic measures. Here, we utilized the murine model of intradermal infection and determined that the aggregative phenotype of
C. auris
as the result of
ACE2
gene deletion elicits potential innate and adaptive immune responses in mice. These observations will help explain the differences in the skin colonization and immune responses of the aggregative morphotype of
C. auris
and open the door to developing novel antifungal therapeutics.
Intranasal administration of
Clostridium butyricum
and its derived extracellular vesicles alleviate LPS-induced acute lung injury
Authors: Liu Li , Zheng Cihua , Xu Zhenyang , Wang Zhuoya , Zhong Yuchun , He Zhidong , Zhang Wenming , Zhang Yuanbing
Published: October 2024

Acute lung injury (ALI) is associated with high morbidity and mortality rates. However, its clinical treatment is limited. Currently, the treatment of lung diseases by regulating the lung microbiota has become a research hotspot. In this study, we investigated the protective effects of the intranasal administration of
Clostridium butyricum
and its derived extracellular vesicles (EVs) against lipopolysaccharide (LPS)-induced ALI. The results demonstrated that compared with the LPS group, the pre-treatment group with
C. butyricum
and its EVs reduced the expression of pro-inflammatory cytokines and alleviated the symptoms in ALI mice by inhibiting the TLR4/MyD88 signaling pathway. Moreover,
C. butyricum
and its derived EVs inhibited the expression of apoptosis-related proteins and increased the expression of lung barrier proteins. Additionally, the intervention of
C. butyricum
changed the composition of the pulmonary microbiota. At the species level, LPS significantly increased the relative abundance of
Acinetobacter johnsonii
, while
C. butyricum
reversed this effect. In conclusion, these data demonstrate that intranasal administration of
C. butyricum
and its EVs can prevent LPS-induced ALI by reducing inflammation, inhibiting apoptosis, and improving lung barrier function. Additionally,
C. butyricum
regulated the pulmonary microbiota of mice to alleviate LPS-induced ALI.

IMPORTANCE

The disorder of pulmonary microbiota plays an important role in the progression of acute lung injury (ALI). However, very few studies have been conducted to treat ALI by modulating pulmonary microbiota. In this study, the diversity and composition of pulmonary microbiota were altered in lipopolysaccharide (LPS)-induced ALI mice, but the ecological balance of the pulmonary microbiota was restored by intranasal administration of
Clostridium butyricum
. Moreover, the study reported the mechanism of
C. butyricum
and its derived extracellular vesicles for the treatment of LPS-induced ALI. These results reveal the importance of pulmonary microbiota in ALI disease. It provides a new approach for the treatment of ALI with new-generation probiotics.
Distinguishing fault offset from climatically modulated channel deflections: Insights from the Pearblossom slip-rate site, Mojave section of the San Andreas fault, California, USA
Authors: Anderson-Merritt Emery O. , Cowgill Eric , Keen-Zebert Amanda , Young Elaine K. , Dailey Mary
Published: October 2024

Fault slip histories are essential for understanding seismic hazard and regional fault system development but fundamentally depend on identifying, dating, and reconstructing displaced markers. Here, we use a case study of the Pearblossom site along the Mojave section of the San Andreas fault in California (USA) to show how pulses of sediment aggradation during wet periods can complicate such reconstructions by producing “imposter offsets”—landforms that develop with an initial deflection that is easily misread as tectonic displacement caused by fault slip. Specifically, we document two channels on the downstream side of the fault: a subtle one that we interpret to have been beheaded and displaced 24–49 m from a source channel on the upstream side of the fault, and a second and more prominent one that we interpret as an imposter offset of 36–88 m. Using optically stimulated luminescence dating, we determine that the source channel incised between 1.44 ± 0.43 ka and 1.27 ± 0.18 ka with a subsequent phase of alluvial fan aggradation at ~0.6 ka, when the channel with the imposter offset formed. Because the pulse of fan deposition coincides temporally with a wet period in Southern California precipitation records, we attribute formation of the imposter offset and the alluvial fan into which it incised to climatically modulated deposition at the site. Comparing precipitation records with charcoal ages compiled from multiple Mojave Desert region locations suggests that other slip-rate sites may be similarly affected. Although climatic effects can complicate slip-rate studies, we show that the morphology and upstream position of the deflected channel can indicate whether a site likely records useful information about fault slip.
Supplemental Material: Influence of flow discharge and minibasin shape on the flow behavior and depositional mechanics of ponded turbidity currents
Authors: Reece J. Kevin , al. et
Published: October 2024

Videos S1–S5.
Cascade testing effectively identifies undiagnosed sickle cell disease in The Gambia: a quality improvement project
Authors: Deans-Louis Etienne , Allen Angela , Allen Stephen John
Published: October 2024

Objective

Sickle cell disease (SCD) has a high mortality during childhood in many low and middle-income countries (LMICs). Early diagnosis improves outcomes but newborn screening is not well established in LMICs. Cascade testing may be feasible and effective in identifying undiagnosed SCD and carriers of haemoglobin (Hb) S.

Design

Quality improvement project using existing clinic and laboratory resources.

Setting

The Haematology Clinic at the Edward Francis Small Teaching Hospital, Banjul, The Gambia.

Participants

Families of index cases with SCD.

Methods

Hb phenotype was determined in full or half-siblings of a SCD index case over a 6-week period using the HemoTypeSC test and confirmed by Hb electrophoresis.

Main outcome measure

Identifying undiagnosed SCD.

Results

Of 102 families invited, 31 (30%) attended during the study period and 53 siblings were tested. Except for one indeterminate test, HemoType SC agreed with Hb electrophoresis. Ten (19%; 95% CI 10 to 32) siblings were diagnosed with HbSS, 25 (47%; 34 to 60) as carriers (HbAS) and 18 (34%; 23 to 48) were unaffected (HbAA). Some symptoms and signs of SCD occurred significantly more frequently in HbSS than in HbAA and HbAS, but none was sufficiently common to help in identifying children for testing.

Conclusions

Cascade testing was effective in identifying undiagnosed HbSS as well as children carrying the sickle cell gene. In routine care settings in LMICs, cascade testing facilitated by point-of-care tests may be feasible and affordable in increasing the detection of SCD and improving outcomes through earlier diagnosis.
Pulmonary hypertension with severe sepsis in ehrlichiosis: what you should know before you hike
Authors: Macasaet Raymart , Khalid Farhan , Bhide Poorva Prashant , Fish Peter
Published: October 2024

Ehrlichiosis is a tickborne illness that can lead to an increased risk of death without appropriate treatment. According to Centers for Disease Control and Prevention, there has been a rise in incidence. We present a case of an immunocompetent patient who reported tick removal after hiking. Chest imaging showed pulmonary vascular congestion, extensive bilateral airspace and bibasilar moderate-dependent pleural effusions. Transthoracic echocardiography showed moderate pulmonary hypertension with right ventricular systolic pressure of 56.3 mm Hg.Ehrlichia chaffeensisPCR testing came back positive. Doxycycline was started in the emergency department and continued for 14 days. The patient had a resolution of the pulmonary hypertension and decrease in tricuspid regurgitation. However, mild mitral regurgitation was persistent. The pulmonary hypertension may be caused by the patient’s response to ehrlichiosis infection, but it may also be explained by the development of acute respiratory distress syndrome, which has been documented in multiple studies.
Impact of a national tsetse control programme to eliminate Gambian sleeping sickness in Uganda: a spatiotemporal modelling study
Authors: Longbottom Joshua , Esterhuizen Johan , Hope Andrew , Lehane Michael J , Mangwiro TN Clement , Mugenyi Albert , Dunkley Sophie , Selby Richard , Tirados Inaki , Torr Steve J , Stanton Michelle C
Published: October 2024

Introduction

Tsetse flies (Glossina) transmitTrypanosoma brucei gambiense, which causes gambiense human African trypanosomiasis (gHAT). As part of national efforts to eliminate gHAT as a public health problem, Uganda implemented a large-scale programme of deploying Tiny Targets, which comprise panels of insecticide-treated material which attract and kill tsetse. At its peak, the programme was the largest tsetse control operation in Africa. Here, we quantify the impact of Tiny Targets and environmental changes on the spatial and temporal patterns of tsetse abundance across North-Western Uganda.

Methods

We leverage a 100-month longitudinal dataset detailingGlossina fuscipes fuscipescatches from monitoring traps between October 2010 and December 2019 within seven districts in North-Western Uganda. We fitted a boosted regression tree (BRT) model assessing environmental suitability, which was used alongside Tiny Target data to fit a spatiotemporal geostatistical model predicting tsetse abundance across our study area (~16 000 km2). We used the spatiotemporal model to quantify the impact of Tiny Targets and environmental changes on the distribution of tsetse, alongside metrics of uncertainty.

Results

Environmental suitability across the study area remained relatively constant over time, with suitability being driven largely by elevation and distance to rivers. By performing a counterfactual analysis using the fitted spatiotemporal geostatistical model, we show that deployment of Tiny Targets across an area of 4000 km2reduced the overall abundance of tsetse to low levels (median daily catch=1.1 tsetse/trap, IQR=0.85–1.28). No spatial–temporal locations had high (>10 tsetse/trap/day) numbers of tsetse compared with 18% of locations for the counterfactual.

Conclusions

In Uganda, Tiny Targets reduced the abundance ofG. f. fuscipesand maintained tsetse populations at low levels. Our model represents the first spatiotemporal geostatistical model investigating the effects of a national tsetse control programme. The outputs provide important data for informing next steps for vector control and surveillance.
Cost and cost-effectiveness of digital technologies for support of tuberculosis treatment adherence: a systematic review
Authors: Kafie Cedric , Mohamed Mona Salaheldin , Zary Miranda , Chilala Chimweta Ian , Bahukudumbi Shruti , Gore Genevieve , Foster Nicola , Fielding Katherine L , Subbaraman Ramnath , Schwartzman Kevin
Published: October 2024

Background

Digital adherence technologies (DATs) may provide a patient-centred approach to supporting tuberculosis (TB) medication adherence and improving treatment outcomes. We synthesised evidence addressing costs and cost-effectiveness of DATs to support TB treatment.

Methods

A systematic review (PROSPERO-CRD42022313531) identified relevant literature from January 2000 to April 2023 in MEDLINE, Embase, CENTRAL, CINAHL, Web of Science along with preprints from medRxiv, Europe PMC and ClinicalTrials.gov. Studies with observational, experimental or quasi-experimental designs (minimum 20 participants) and modelling studies reporting quantitative data on the cost or cost-effectiveness of DATs for TB infection or disease treatment were included. Study characteristics, cost and cost-effectiveness outcomes were extracted.

Results

Of 3619 titles identified by our systematic search, 29 studies met inclusion criteria, of which 9 addressed cost-effectiveness. DATs included short message service (SMS) reminders, phone-based technologies, digital pillboxes, ingestible sensors and video-observed therapy (VOT). VOT was the most extensively studied (16 studies) and was generally cost saving when compared with healthcare provider directly observed therapy (DOT), particularly when costs to patients were included—though findings were largely from high-income countries. Cost-effectiveness findings were highly variable, ranging from no clinical effect in one study (SMS), to greater effectiveness with concurrent cost savings (VOT) in others. Only eight studies adequately reported at least 80% of the elements required by Consolidated Health Economic Evaluation Reporting Standards, a standard reporting checklist for health economic evaluations.

Conclusion

DATs may be cost saving or cost-effective compared with healthcare provider DOT, particularly in high-income settings. However, more data of higher quality are needed, notably in lower-income and middle-income countries which have the greatest TB burden.
The PHA4GE Microbial Data-Sharing Accord: establishing baseline consensus microbial data-sharing norms to facilitate cross-sectoral collaboration
Authors: Griffiths Emma J , van Heusden Peter , Tamuhla Tsaone , Lulamba Eddie T , Bedeker Anja , Nichols Michelle , Christoffels Alan , Tiffin Nicki
Published: October 2024

Microbial data sharing underlies evidence-based microbial research, as well as pathogen surveillance and analysis essential to public health. While the need for data sharing was highlighted during the SARS-CoV-2 pandemic, some concerns regarding secondary data use have also surfaced. Although general guidelines are available for data sharing, we note the absence of a set of established, universal, unambiguous and accessible principles to guide the secondary use of microbial data. Here, we propose the Public Health Alliance for Genomic Epidemiology (PHA4GE) Microbial Data-Sharing Accord to consolidate consensus norms and accepted practices for the secondary use of microbial data. The Accord provides a set of seven simple, baseline principles to address key concerns that may arise for researchers providing microbial datasets for secondary use and to guide responsible use by data users. By providing clear rules for secondary use of microbial data, the Accord can increase confidence in sharing by data providers and protect against data mis-use during secondary analyses.
Characteristics of non-randomised studies of drug treatments: cross sectional study
Authors: Yaacoub Sally , Porcher Raphael , Pellat Anna , Bonnet Hillary , Tran Viet-Thi , Ravaud Philippe , Boutron Isabelle
Published: October 2024

Objective

To examine the characteristics of comparative non-randomised studies that assess the effectiveness or safety, or both, of drug treatments.

Design

Cross sectional study.

Data sources

Medline (Ovid), for reports published from 1 June 2022 to 31 August 2022.

Eligibility criteria for selecting studies

Reports of comparative non-randomised studies that assessed the effectiveness or safety, or both, of drug treatments were included. A randomly ordered sample was screened until 200 eligible reports were found.Data on general characteristics, reporting characteristics, and time point alignment were extracted, and possible related biases,witha piloted form inspired by reporting guidelines and the target trial emulation framework.

Results

Of 462 reports of non-randomised studies identified, 262 studies were excluded (32% had no comparator and 25% did not account for confounding factors). To assess time point alignment and possible related biases, three study time points were considered: eligibility, treatment assignment, and start of follow-up. Of the 200 included reports, 70% had one possible bias, related to: inclusion of prevalent users in 24%, post-treatment eligibility criteria in 32%, immortal time periods in 42%, and classification of treatment in 23%. Reporting was incomplete, and only 2% reported all six of the key elements considered: eligibility criteria (87%), description of treatment (46%), deviations in treatment (27%), causal contrast (11%), primary outcomes (90%), and confounding factors (88%). Most studies used routinely collected data (67%), but only 7% reported using validation studies of the codes or algorithms applied to select the population. Only 7% of reports mentioned registration on a trial registry and 3% had an available protocol.

Conclusions

The findings of the study suggest that although access to real world evidence could be valuable, the robustness and transparency of non-randomised studies need to be improved.