Displaying publications 21 - 29 of 29 in total

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  1. Dooley NL, Chabikwa TG, Pava Z, Loughland JR, Hamelink J, Berry K, et al.
    Nat Commun, 2023 Nov 15;14(1):7387.
    PMID: 37968278 DOI: 10.1038/s41467-023-43181-7
    Plasmodium falciparum malaria drives immunoregulatory responses across multiple cell subsets, which protects from immunopathogenesis, but also hampers the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analyse the immune landscape with single cell RNA sequencing during P. falciparum malaria. We identify cell type specific responses in sub-clustered major immune cell types. Malaria is associated with an increase in immunosuppressive monocytes, alongside NK and γδ T cells which up-regulate tolerogenic markers. IL-10-producing Tr1 CD4 T cells and IL-10-producing regulatory B cells are also induced. Type I interferon responses are identified across all cell types, suggesting Type I interferon signalling may be linked to induction of immunoregulatory networks during malaria. These findings provide insights into cell-specific and shared immunoregulatory changes during malaria and provide a data resource for further analysis.
  2. Kho S, Barber BE, Johar E, Andries B, Poespoprodjo JR, Kenangalem E, et al.
    Blood, 2018 Sep 20;132(12):1332-1344.
    PMID: 30026183 DOI: 10.1182/blood-2018-05-849307
    Platelets are understood to assist host innate immune responses against infection, although direct evidence of this function in any human disease, including malaria, is unknown. Here we characterized platelet-erythrocyte interactions by microscopy and flow cytometry in patients with malaria naturally infected with Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, or Plasmodium knowlesi Blood samples from 376 participants were collected from malaria-endemic areas of Papua, Indonesia, and Sabah, Malaysia. Platelets were observed binding directly with and killing intraerythrocytic parasites of each of the Plasmodium species studied, particularly mature stages, and was greatest in P vivax patients. Platelets preferentially bound to the infected more than to the uninfected erythrocytes in the bloodstream. Analysis of intraerythrocytic parasites indicated the frequent occurrence of platelet-associated parasite killing, characterized by the intraerythrocytic accumulation of platelet factor-4 and terminal deoxynucleotidyl transferase deoxyuridine triphosphate nick-end labeling of parasite nuclei (PF4+TUNEL+ parasites). These PF4+TUNEL+ parasites were not associated with measures of systemic platelet activation. Importantly, patient platelet counts, infected erythrocyte-platelet complexes, and platelet-associated parasite killing correlated inversely with patient parasite loads. These relationships, taken together with the frequency of platelet-associated parasite killing observed among the different patients and Plasmodium species, suggest that platelets may control the growth of between 5% and 60% of circulating parasites. Platelet-erythrocyte complexes made up a major proportion of the total platelet pool in patients with malaria and may therefore contribute considerably to malarial thrombocytopenia. Parasite killing was demonstrated to be platelet factor-4-mediated in P knowlesi culture. Collectively, our results indicate that platelets directly contribute to innate control of Plasmodium infection in human malaria.
  3. Murdiyarso LS, Rajahram GS, Tan AF, Piera KA, William T, Oyong DA, et al.
    Am J Trop Med Hyg, 2025 Jan 08;112(1):85-88.
    PMID: 39531730 DOI: 10.4269/ajtmh.24-0264
    Zoonotic malaria presents a major public health challenge in Southeast Asia. Plasmodium cynomolgi coinfects the same macaque hosts and mosquito vectors as the most common cause of zoonotic malaria, Plasmodium knowlesi. Plasmodium cynomolgi appears morphologically similar to Plasmodium vivax on microscopy and can amplify P. vivax polymerase chain reaction (PCR) assays, confounding transmission estimates. We screened 2,103 samples for P. cynomolgi across all 26 districts in Sabah, Malaysia, from 2010 to 2021. Samples comprised 1,425 P. knowlesi, 256 P. vivax, 293 P. falciparum, and 31 Plasmodium malariae PCR-confirmed malaria cases and 100 malaria microscopy-positive and species-specific PCR-negative samples. A nested PCR assay targeting P. cynomolgi-specific 18S small subunit ribosomal ribonucleic acid with a detection limit of ∼2 parasites/µL was conducted on whole blood samples. No P. cynomolgi infections were detected. Symptomatic P. cynomolgi co-infections appear rare in Malaysia, although prevalence may be underestimated owing to the absence of routine molecular screening and the sensitivity of available assays.
  4. Kim ARJ, Hon YK, Guan CA, Lai WH, Bujang MA, Peter S, et al.
    Med J Malaysia, 2025 Jan;80(1):81-87.
    PMID: 39812433
    INTRODUCTION: Second victim experience (SVE) refers to the emotional and psychological impact experienced by healthcare providers who are involved in patient safety incidents (PSIs). Despite growing awareness of patient safety in healthcare organizations, remedial actions often focus only on the first victim, the patient. Therefore, it is important to recognize and address the emotional and physical toll that PSIs to ensure the well-being of and to promote a culture of safety in healthcare settings. Hence, this study was initiated to determine the prevalence of SVE, assess symptoms related to SVE and evaluate the level of support needed by healthcare providers.

    MATERIALS AND METHODS: The Second Victim Experience and Support Tool for Recovery (SVEST-R) questionnaire was utilized to conduct an anonymous survey on the healthcare providers in Sarawak General Hospital (SGH) from August to October 2018.

    RESULTS: A total of 482 respondents participated in the survey and 46.1% of the respondents reported SVE following their involvement in PSIs. Notably, symptoms such as flashbacks, fear, and stress tend to persist for longer durations compared to other symptoms. It is worth noting that non-work-related support received the highest mean (medical doctors = 3.83; nurses = 3.70), indicating that respondents preferred to seek emotional support from their friends and families. Furthermore, nurses reported a significantly higher experience of absenteeism following PSIs than doctors (p=0.003). In addition, most respondents expressed a desire for discussion or counselling with a respected peer or supervisor following their involvement in PSIs.

    CONCLUSION: Present study reported a relatively high prevalence of SVE among healthcare providers at SGH. Hence, proactive measures, including non-work related and supervisor support, are essential in facilitating their overall well-being and successful recovery.

  5. Longley RJ, Grigg MJ, Schoffer K, Obadia T, Hyslop S, Piera KA, et al.
    Cell Rep Med, 2022 06 21;3(6):100662.
    PMID: 35732155 DOI: 10.1016/j.xcrm.2022.100662
    Serological markers are a promising tool for surveillance and targeted interventions for Plasmodium vivax malaria. P. vivax is closely related to the zoonotic parasite P. knowlesi, which also infects humans. P. vivax and P. knowlesi are co-endemic across much of South East Asia, making it important to design serological markers that minimize cross-reactivity in this region. To determine the degree of IgG cross-reactivity against a panel of P. vivax serological markers, we assayed samples from human patients with P. knowlesi malaria. IgG antibody reactivity is high against P. vivax proteins with high sequence identity with their P. knowlesi ortholog. IgG reactivity peaks at 7 days post-P. knowlesi infection and is short-lived, with minimal responses 1 year post-infection. We designed a panel of eight P. vivax proteins with low levels of cross-reactivity with P. knowlesi. This panel can accurately classify recent P. vivax infections while reducing misclassification of recent P. knowlesi infections.
  6. Braima KA, Piera KA, Lubis IND, Noviyanti R, Rajahram GS, Kariodimedjo P, et al.
    PLoS Negl Trop Dis, 2025 Feb;19(2):e0012129.
    PMID: 39913530 DOI: 10.1371/journal.pntd.0012129
    BACKGROUND: Zoonotic P. knowlesi and P. cynomolgi symptomatic and asymptomatic infections occur across endemic areas of Southeast Asia. Most infections are low-parasitemia, with an unknown proportion below routine microscopy detection thresholds. Molecular surveillance tools optimizing the limit of detection (LOD) would allow more accurate estimates of zoonotic malaria prevalence.

    METHODOLOGY/PRINCIPAL FINDINGS: An established ultra-sensitive Plasmodium genus quantitative-PCR (qPCR) assay targeting the 18S rRNA gene underwent LOD evaluation with and without reverse transcription (RT) for P. knowlesi, P. cynomolgi and P. vivax using total nucleic acid preserved (DNA/RNA Shield) isolates and archived dried blood spots (DBS). LODs for selected P. knowlesi-specific assays, and reference P. vivax- and P. cynomolgi-specific assays were determined with reverse transcription (RT). Assay specificities were assessed using clinical malaria samples and malaria-negative controls. The use of reverse transcription improved Plasmodium species detection by up to 10,000-fold (Plasmodium genus), 2759-fold (P. knowlesi) and 1000-fold (P. vivax and P. cynomolgi). The Kamau et al. Plasmodium genus RT-qPCR assay was highly sensitive for P. knowlesi detection with a median LOD of ≤0.0002 parasites/μL compared to 0.002 parasites/μL for P. cynomolgi and P. vivax. The LODs with RT for P. knowlesi-specific PCRs were enhanced for the Imwong et al. 18S rRNA (0.0007 parasites/μL) and Divis et al. real-time 18S rRNA (0.0002 parasites/μL) assays, but not for the Lubis et al. hemi-nested SICAvar (1.1 parasites/μL) and Lee et al. nested 18S rRNA (11 parasites/μL). The LOD for P. vivax- and P. cynomolgi-specific assays with RT were moderately improved at 0.02 and 0.002 parasites/μL, respectively (1000-fold change). For DBS P. knowlesi samples the use of RT also markedly improved the Plasmodium genus qPCR LOD from 19.89 to 0.08 parasites/μL (249-fold change); no LOD improvement was demonstrated in DBS archived beyond 6 years. The Plasmodium genus and P. knowlesi-assays were 100% specific for Plasmodium species and P. knowlesi detection, respectively, from 190 clinical infections and 48 healthy controls. Reference P. vivax-specific primers demonstrated known cross-reactivity with P. cynomolgi.

    CONCLUSIONS/SIGNIFICANCE: Our findings support the use of an 18S rRNA Plasmodium genus qPCR and species-specific nested PCR protocol with RT for highly-sensitive surveillance of zoonotic and human Plasmodium species infections.

  7. Braima KA, Piera KA, Lubis IN, Noviyanti R, Rajahram GS, Kariodimedjo P, et al.
    medRxiv, 2024 Apr 06.
    PMID: 38633782 DOI: 10.1101/2024.04.04.24305339
    BACKGROUND: Zoonotic P. knowlesi and P. cynomolgi symptomatic and asymptomatic infections occur across endemic areas of Southeast Asia. Most infections are low-parasitemia, with an unknown proportion below routine microscopy detection thresholds. Molecular surveillance tools optimizing the limit of detection (LOD) would allow more accurate estimates of zoonotic malaria prevalence.

    METHODS: An established ultra-sensitive Plasmodium genus quantitative-PCR (qPCR) assay targeting the 18S rRNA gene underwent LOD evaluation with and without reverse transcription (RT) for P. knowlesi, P. cynomolgi and P. vivax using total nucleic acid preserved (DNA/RNA Shield™) isolates and archived dried blood spots (DBS). LODs for selected P. knowlesi-specific assays, and reference P. vivax- and P. cynomolgi-specific assays were determined with RT. Assay specificities were assessed using clinical malaria samples and malaria-negative controls.

    RESULTS: The use of reverse transcription improved Plasmodium species detection by up to 10,000-fold (Plasmodium genus), 2759-fold (P. knowlesi), 1000-fold (P. vivax) and 10-fold (P. cynomolgi). The median LOD with RT for the Kamau et al. Plasmodium genus RT-qPCR assay was ≤0.0002 parasites/μL for P. knowlesi and 0.002 parasites/μL for both P. cynomolgi and P. vivax. The LODs with RT for P. knowlesi-specific PCRs were: Imwong et al. 18S rRNA (0.0007 parasites/μL); Divis et al. real-time 18S rRNA (0.0002 parasites/μL); Lubis et al. hemi-nested SICAvar (1.1 parasites/μL) and Lee et al. nested 18S rRNA (11 parasites/μL). The LOD for P. vivax- and P. cynomolgi-specific assays with RT were 0.02 and 0.20 parasites/μL respectively. For DBS P. knowlesi samples the median LOD for the Plasmodium genus qPCR with RT was 0.08, and without RT was 19.89 parasites/uL (249-fold change); no LOD improvement was demonstrated in DBS archived beyond 6 years. The Plasmodium genus and P. knowlesi-assays were 100% specific for Plasmodium species and P. knowlesi detection, respectively, from 190 clinical infections and 48 healthy controls. Reference P. vivax-specific primers demonstrated known cross-reactivity with P. cynomolgi.

    CONCLUSION: Our findings support the use of an 18S rRNA Plasmodium genus qPCR and species-specific nested PCR protocol with RT for highly-sensitive surveillance of zoonotic and human Plasmodium species infections.

  8. Nedoluzhko A, Vergasova E, Sharko F, Agapitova N, Kharitonov D, Sukhanova X, et al.
    BMC Genomics, 2025 Mar 05;26(1):220.
    PMID: 40045199 DOI: 10.1186/s12864-025-11361-y
    BACKGROUND: In the Ist millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style and economy can be traced to the eastern part of this steppe "corridor", primarily to the territory of the present-day Republic of Tuva in Russia. Here, in the Turan-Uyuk Basin, also known as the "Valley of the Kings", some of the earliest known Scythian-type archaeological sites called Arzhan-1, Arzhan-2, Chinge-Tey I, Tunnug 1 were studied. Each of them is a large-scale funerary commemorative complex with burials of tribal nomadic leaders, surrounded by graves of supposed members of their families or associates. All these people belonged to the societies which are associated with the earliest nomadic cultures in Asia. Representatives of similar cultures will later be known and described as the Scythians/the Saka in Assyrian, Achaemenid, and Greek sources. Arzhan 2 and Chinge-Tey I elite level sites as well as ordinary pastoralist burials of the early-Scythian period in Tuva are attributed to the Aldy-Bel archaeological culture of the Early Iron Age (8th- 6th century BC). Taking the first step to shed light on the genetic origin of Aldy-Bel elites, we carried out a comparative genome-wide analysis of an elite level person buried in grave 9 at Chinge-Tey I (7th- 6th centuries BC) and two published earlier genomes of individuals, whose burials (graves 14 and 22) accompanied the 'royal couple' (grave 5) at Arzhan-2. This study aims also at checking a hypothesis of genetic kinship between human individuals buried in the large-scale burial complexes of the "Valley of the Kings" and brings up the issue of possible dynastic connections of local elites, buried under different kurgans of the valley.

    RESULTS: First, ancient DNA analysis of an elite nomadic warrior from Chinge-Tey I has been carried out, thus a third wide-genome dataset for Aldy-Bel culture- one of the earliest nomadic cultures in Asia, is presented in this study. Second, we undertook a comparative analysis of genome-wide data of three mentioned Aldy-Bel culture representatives and individuals of the other Bronze and Early Iron Age population groups of Asia to estimate their possible genetic connections. Then, kinship analysis was undertaken for these three Aldy-Bel culture individuals. Finally, mitochondrial and Y-chromosome haplogroups of Chinge-Tey princely person were compared to those of other Aldy-Bel culture representatives and to individuals of subsequent Scythian-type Uyuk-Sagly culture in Tuva.

    CONCLUSION: (1) Generating the third wide-genome of the enabled us to undertake its comparison with two other genomes of Aldy-Bel culture representatives (Arzhan-2, graves 14 and 22) and with other Bronze and Early Iron Age population groups in Asia to trace the origin and genetic connection of Aldy-Bel population, representing one of the earliest Scythian-type nomadic group. (2) The results obtained show that the princely individual from Chinge-Tey I and two 'king's associates' from Arzhan-2 were genetically close to nomads of simultaneous Tasmola culture in Eastern and Central Kazakhstan and pastoralists buried in the Early Iron Age cemeteries of present-day Xinjiang (first of all, Abusanteer archaeological site). Aldy-Bel culture representatives appeared also close to individuals of the Middle Bronze Age Okunevo culture in the Minusinsk Basin. Besides, Aldy-Bel pastoralists turned out genetically close to nomads of the subsequent Uyuk-Sagly culture in Mongolia (5th - 3rd centuries BC). (3) Ancient DNA kinship analyses, undertaken for three Aldy-Bel culture individuals pointed out to the absence of their tribe kinship. (4) On the other hand, Chinge-Tey warrior's mitochondrial haplogroup G was previously described in two (graves 14 and 5) individuals from Arzhan-2, including a female individual from the "royal" tomb 5. This result provided a possibility of maternal kinship among this so called 'queen' from Arzhan-2 and the princely person from Chinge-Tey I. This possibility supported a hypothesis of their family ties suggested on archaeological materials. Y-chromosome haplogroup Q1b1, revealed for the princely person, was widely distributed among local people of Aldy-Bel and subsequent Uyuk-Sagly cultures.

  9. Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
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