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Article ; Online: Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route.

Barbarić, Lucija / Horjan-Zanki, Ivana

2022

Abstract: Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains ... ...

Abstract	Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.
Language	English
Publishing date	2022-04-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1055109-8
ISSN	1437-1596 ; 0937-9827
ISSN (online)	1437-1596
ISSN	0937-9827
DOI	10.1007/s00414-022-02829-7
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Article ; Online: Assessing Cell Competition in Human Pluripotent Stem Cell (hPSC) Cultures.

Price, Christopher J / Barbaric, Ivana

Current protocols

2022 Volume 2, Issue 5, Page(s) e435

Abstract: Cell-cell interactions are required for development and homeostasis in multicellular organisms from insects to mammals. A critical process governed by these interactions is cell competition, which functions throughout development to control tissue ... ...

Abstract	Cell-cell interactions are required for development and homeostasis in multicellular organisms from insects to mammals. A critical process governed by these interactions is cell competition, which functions throughout development to control tissue composition by eliminating cells that possess a lower fitness status than their neighbors. Human pluripotent stem cells (hPSCs) are a key biological tool in modeling human development and offer further potential as a source of clinically relevant cell populations for regenerative medicine applications. Recently, cell competition has been demonstrated in hPSC cultures and during induced pluripotent stem cell reprogramming. In turn, these findings suggest that hPSCs can be used as a tool to study and model cell-cell interactions during different stages of development and disease. Here, we provide a panel of protocols optimized for hPSCs to investigate the potential role that cell competition may have in determining the fate and composition of cell populations during culture. The protocols entail assessment of the competitive phenotype and the mode through which cell competition may lead to elimination of less-fit cells from mosaic cultures with fitter counterparts. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Electroporation of hPSCs to establish a fluorescent reference cell line Support Protocol 1: Single-cell dissociation of hPSCs Support Protocol 2: Single-cell cloning of fluorescently labeled hPSCs Basic Protocol 2: Separate culture and co-culture proliferation assays Basic Protocol 3: Assessing levels of apoptosis in hPSC cultures using flow cytometry Basic Protocol 4: Transwell assay Support Protocol 3: Immunohistochemistry and image quantification of cleaved caspase-3 Basic Protocol 5: Cell confrontation assay Basic Protocol 6: Cell compression assay Basic Protocol 7: Time-lapse imaging to assess mechanical extrusion.
MeSH term(s)	Animals ; Cell Competition ; Flow Cytometry/methods ; Humans ; Induced Pluripotent Stem Cells ; Mammals ; Pluripotent Stem Cells ; Regenerative Medicine
Language	English
Publishing date	2022-05-27
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.435
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Article ; Online: Human whole mitochondrial genome sequencing and analysis: optimization of the experimental workflow.

Sukser, Viktorija / Korolija, Marina / Račić, Ivana / Rožić, Sara / Barbarić, Lucija

Croatian medical journal

2022 Volume 63, Issue 3, Page(s) 224–230

Abstract: Aim: To evaluate critical steps in Illumina® Human mtDNA Genome assay: target enrichment, limited-cycle PCR, and library normalization, in order to optimize the protocol for analysis of whole mitochondrial genomes from human reference samples.: ... ...

Abstract	Aim: To evaluate critical steps in Illumina® Human mtDNA Genome assay: target enrichment, limited-cycle PCR, and library normalization, in order to optimize the protocol for analysis of whole mitochondrial genomes from human reference samples. Methods: Three long-range high-fidelity DNA polymerases (PlatinumTM PCR SuperMix High Fidelity, LA Taq® Hot Start, and PrimeSTAR® GXL) were tested for their performance in the amplification of mtDNA fragments. Sequencing results of ten samples, as well as negative controls, which underwent library preparation with 12 and 15 cycles in limited-cycle PCR were compared. Additionally, two library normalization methods were compared: bead-based normalization vs quantification and individual normalization. Results: PrimeSTAR® GXL performed best for mitochondrial DNA enrichment. Increment of amplification cycles to 15 in limited-cycle PCR step did not affect either the sequencing process or variant calling. Library quantification combined with individual library-by-library dilution outperformed bead-based normalization. Conclusion: Optimizations described herein provide beneficial insights for laboratories aiming at implementation and/or advancement of similar massively parallel sequencing workflows (eg, small genomes, PCR amplicons, and plasmids).
MeSH term(s)	DNA, Mitochondrial/genetics ; Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Workflow
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2022-06-13
Publishing country	Croatia
Document type	Journal Article
ZDB-ID	1157623-6
ISSN	1332-8166 ; 0353-9504
ISSN (online)	1332-8166
ISSN	0353-9504
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Article ; Online: Characterizing the Genetic Stability of Human Naïve and Primed Pluripotent Stem Cells.

Baker, Duncan / Barbaric, Ivana

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2416, Page(s) 267–284

Abstract: The presence of genetic changes in human pluripotent stem cells (hPSCs) can affect their behavior and impact on the utility of hPSC-based applications in research and clinic. The spectrum of spontaneously arising genetic abnormalities in hPSCs is wide ... ...

Abstract	The presence of genetic changes in human pluripotent stem cells (hPSCs) can affect their behavior and impact on the utility of hPSC-based applications in research and clinic. The spectrum of spontaneously arising genetic abnormalities in hPSCs is wide and ranges from numerical and structural chromosomal anomalies down to point mutations. The detection of genetic changes in hPSCs is confounded by the fact that no single method detects all types of abnormalities with the same accuracy and sensitivity, therefore necessitating the use of a combination of different methods. Here, we provide detailed protocols for two methods commonly utilized for the detection of genetic changes in naïve and primed hPSCs: karyotyping by G-banding and fluorescent in situ hybridization (FISH).
MeSH term(s)	Cell Differentiation ; Chromosome Aberrations ; Chromosome Banding ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Pluripotent Stem Cells
Language	English
Publishing date	2021-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1908-7_17
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Article ; Online: Fitness selection in human pluripotent stem cells and interspecies chimeras: Implications for human development and regenerative medicine.

Wu, Jun / Barbaric, Ivana

Developmental biology

2021 Volume 476, Page(s) 209–217

Abstract: A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could ... ...

Abstract	A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could lead to congenital defects or embryonic lethality and pose a risk of being transmitted to future generations. The observation that genetic errors are relatively common in preimplantation embryos, but their levels reduce as development progresses, suggests the existence of mechanisms for clearance of aberrant, unfit or damaged cells. Although early human embryogenesis is largely experimentally inaccessible, pluripotent stem cell (PSC) lines can be derived either from the inner cell mass (ICM) of a blastocyst or by reprogramming somatic cells into an embryonic stem cell-like state. PSCs retain the ability to differentiate into any cell type in vitro and, hence, they represent a unique and powerful tool for studying otherwise intractable stages of human development. The advent of PSCs has also opened up a possibility of developing regenerative medicine therapies, either through PSC differentiation in vitro or by creating interspecies chimeras for organ replacement. Here, we discuss the emerging evidence of cell selection in human PSC populations in vivo and in vitro and we highlight the implications of understanding this phenomenon for human development and regenerative medicine.
MeSH term(s)	Animals ; Blastocyst/metabolism ; Cell Differentiation ; Chimera/embryology ; Chimera/genetics ; Embryo, Mammalian ; Embryonic Stem Cells ; Genetic Fitness/genetics ; Genetic Fitness/physiology ; Humans ; Pluripotent Stem Cells/cytology ; Pluripotent Stem Cells/metabolism ; Pluripotent Stem Cells/physiology ; Regenerative Medicine
Language	English
Publishing date	2021-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2021.03.025
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Article ; Online: Modeling the selective growth advantage of genetically variant human pluripotent stem cells to identify opportunities for manufacturing process control.

Beltran-Rendon, Catherine / Price, Christopher J / Glen, Katie / Stacey, Adrian / Barbaric, Ivana / Thomas, Robert J

Cytotherapy

2024 Volume 26, Issue 4, Page(s) 383–392

Abstract: Background aims: The appearance of genetically variant populations in human pluripotent stem cell (hPSC) cultures represents a concern for research and clinical applications. Genetic variations may alter hPSC differentiation potential or cause phenotype ...

Abstract	Background aims: The appearance of genetically variant populations in human pluripotent stem cell (hPSC) cultures represents a concern for research and clinical applications. Genetic variations may alter hPSC differentiation potential or cause phenotype variation in differentiated cells. Further, variants may have properties such as proliferative rate, or response to the culture environment, that differ from wild-type cells. As such, understanding the behavior of these variants in culture, and any potential operational impact on manufacturing processes, will be necessary to control quality of putative hPSC-based products that include a proportion of variant threshold in their quality specification. Methods: Here we show a computational model that mathematically describes the growth dynamics between commonly occurring genetically variant hPSCs and their counterpart wild-type cells in culture. Results: We show that our model is capable of representing the growth behaviors of both wild-type and variant hPSCs in individual and co-culture systems. Conclusions: This representation allows us to identify three critical process parameters that drive critical quality attributes when genetically variant cells are present within the system: total culture density, proportion of variant cells within the culture system and variant cell overgrowth. Lastly, we used our model to predict how the variability of these parameters affects the prevalence of both populations in culture.
MeSH term(s)	Humans ; Cell Culture Techniques ; Pluripotent Stem Cells ; Cell Differentiation/genetics ; Coculture Techniques
Language	English
Publishing date	2024-02-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2039821-9
ISSN	1477-2566 ; 1465-3249
ISSN (online)	1477-2566
ISSN	1465-3249
DOI	10.1016/j.jcyt.2024.01.010
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Article: Fitness selection in human pluripotent stem cells and interspecies chimeras: Implications for human development and regenerative medicine

Wu, Jun / Barbaric, Ivana

Developmental biology. 2021 Aug., v. 476

2021

Abstract	A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could lead to congenital defects or embryonic lethality and pose a risk of being transmitted to future generations. The observation that genetic errors are relatively common in preimplantation embryos, but their levels reduce as development progresses, suggests the existence of mechanisms for clearance of aberrant, unfit or damaged cells. Although early human embryogenesis is largely experimentally inaccessible, pluripotent stem cell (PSC) lines can be derived either from the inner cell mass (ICM) of a blastocyst or by reprogramming somatic cells into an embryonic stem cell-like state. PSCs retain the ability to differentiate into any cell type in vitro and, hence, they represent a unique and powerful tool for studying otherwise intractable stages of human development. The advent of PSCs has also opened up a possibility of developing regenerative medicine therapies, either through PSC differentiation in vitro or by creating interspecies chimeras for organ replacement. Here, we discuss the emerging evidence of cell selection in human PSC populations in vivo and in vitro and we highlight the implications of understanding this phenomenon for human development and regenerative medicine.
Keywords	adults ; blastocyst ; embryogenesis ; embryonic mortality ; human development ; humans ; medicine ; risk ; stem cells
Language	English
Dates of publication	2021-08
Size	p. 209-217.
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2021.03.025
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Article: Numerical study of the flow field around hydrokinetic turbines with winglets on the blades

Barbarić, Marina / Batistić, Ivan / Guzović, Zvonimir

Renewable energy. 2022 June, v. 192

2022

Abstract: Design methods and concepts that can increase the energy conversion efficiency of marine and river current turbines are of great importance for the development and wider utilization of this emerging renewable energy technology. This work is aimed to ... ...

Abstract	Design methods and concepts that can increase the energy conversion efficiency of marine and river current turbines are of great importance for the development and wider utilization of this emerging renewable energy technology. This work is aimed to improve hydrodynamic performances of the hydrokinetic turbines to get as close as possible to the theoretical energy conversion efficiency limitation of 59.3%, known as the Lanchester–Betz–Joukowsky limit. The winglets are integrated at the turbine blade tips to reduce the effect of the tip vortex. The winglet design concept is adopted from the jet aircraft and adjusted to the hydrokinetic turbine application. The numerical investigation of the winglets impact on the hydrodynamic performances was performed using computational fluid dynamic (CFD). The results indicate that winglets subdue the strength of tip vortices, which is reflected through the increase in the power extracted. It has been confirmed that winglet height has a great influence on the power coefficient increase, which for higher winglets reaches the value above 50%. The analysis of the wake regions behind turbines pointed out that the turbines with winglets form stronger vortices in the far wake zone which may influence the back-flow turbine installed in row array.
Keywords	aircraft ; energy conversion ; hydrodynamics ; renewable energy sources ; rivers
Language	English
Dates of publication	2022-06
Size	p. 692-704.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2001449-1
ISSN	1879-0682 ; 0960-1481
ISSN (online)	1879-0682
ISSN	0960-1481
DOI	10.1016/j.renene.2022.04.157
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Article: The impact of biofilm on marine current turbine performance

Farkas, Andrea / Degiuli, Nastia / Martić, Ivana / Barbarić, Marina / Guzović, Zvonimir

Renewable energy. 2022 May, v. 190

2022

Abstract: Although several problems related to biofouling of marine current turbines (MCTs) are reported in the literature, the most important one is related to long-term operational performance and maintenance costs. Nevertheless, studies related to the impact of ...

Abstract	Although several problems related to biofouling of marine current turbines (MCTs) are reported in the literature, the most important one is related to long-term operational performance and maintenance costs. Nevertheless, studies related to the impact of biofouling on MCT performance are rather scarce. In this study, the impact of biofilm on MCT performance is investigated using the Computational Fluid Dynamics (CFD) approach. Biofilm is modelled using previously developed roughness functions implemented in a wall function solver. A verification study is performed to determine sufficient grid spacings and to calculate numerical uncertainty. The validation study is conducted by comparing the obtained results with experimental and numerical ones from the literature. Full-scale CFD simulations are performed for six fouling conditions with varying biofilm height and percentage of surface coverage at eight tip speed ratios (TSRs). The obtained results highlight the significant impact of biofilm on MCT performance reflected in a decrease in the power coefficient, which for the optimal TSR is equal to −10.7% for the R1 fouling condition. Finally, a detailed analysis of the flow around MCTs fouled with biofilm is conducted and the reasons for the detrimental impact of biofilm on MCT performance are discussed.
Keywords	biofilm ; biofouling ; fluid mechanics ; renewable energy sources ; roughness ; uncertainty
Language	English
Dates of publication	2022-05
Size	p. 584-595.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2001449-1
ISSN	1879-0682 ; 0960-1481
ISSN (online)	1879-0682
ISSN	0960-1481
DOI	10.1016/j.renene.2022.03.134
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Article ; Online: HIV, syphilis and hepatitis B prevalence, related risk behaviours and correlates of condom use among transgender women in two cities in Sri Lanka: findings from respondent-driven sampling surveys.

Barbaric, Jelena / Bozicevic, Ivana / Manathunge, Ariyaratne / Gajaweera, Chathrini / Beneragama, Sriyakanthi

Sexual health

2021 Volume 18, Issue 4, Page(s) 311–318

Abstract: Background Biobehavioural data on transgender women (TGW) are limited globally.: Methods: We used data collected as part of the 2017-18 National Integrated HIV Biobehavioural Survey, which included 254 TGW in Colombo and 252 in Jaffna, for structured ... ...

Abstract	Background Biobehavioural data on transgender women (TGW) are limited globally. Methods: We used data collected as part of the 2017-18 National Integrated HIV Biobehavioural Survey, which included 254 TGW in Colombo and 252 in Jaffna, for structured questionnaire interviews and biological testing. We performed multivariable logistic regression analysis to explore factors associated with condom use. Results: We found low HIV prevalence in Colombo (0.6%) and no HIV infections in Jaffna. TGW in Colombo had higher positivity on the Treponema pallidum-particle agglutination test (2.5%) compared with TGW in Jaffna (0.4%). We found no hepatitis B infections. In both cities, <25% of TGW have comprehensive knowledge about HIV prevention. In Colombo 54.4%, but only 21.4% of TGW in Jaffna, have ever been tested for HIV. Drug-injecting behaviours are uncommon in both cities (prevalence <1%), whereas 7.4% reported sharing equipment for injecting feminising hormones in Colombo. Greater proportions of TGW in Colombo compared with Jaffna used condom at last sex (82.3% vs 37.7%). Multivariable analysis showed lower odds of condom use at last sex in TGW aged >30 years and those who did not test for HIV in the past 12 months in Colombo, and for TGW with higher income in Jaffna, TGW not visiting outdoor sites to find partners, and TGW who sold sex. Conclusions: Current burden of HIV, syphilis and hepatitis B among TGW in Sri Lanka is low. Although risk behavioural patterns vary between the cities, a substantial sexually transmitted infection vulnerability is a common denominator, calling for strengthening of the capacity to respond to specific TGW needs.
MeSH term(s)	Cities ; Condoms ; Female ; HIV Infections/epidemiology ; HIV Infections/prevention & control ; Hepatitis B/epidemiology ; Hepatitis B/prevention & control ; Humans ; Prevalence ; Risk-Taking ; Sexual Behavior ; Sri Lanka/epidemiology ; Surveys and Questionnaires ; Syphilis/epidemiology ; Transgender Persons
Language	English
Publishing date	2021-08-26
Publishing country	Australia
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2256731-8
ISSN	1449-8987 ; 1448-5028
ISSN (online)	1449-8987
ISSN	1448-5028
DOI	10.1071/SH21061
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