A5001808519- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Fractal and DNA sequence analysis
- Genomic variations and chromosomal abnormalities
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Pleistocene-Era Hominins and Archaeology
- Genetic diversity and population structure
- Genetics and Neurodevelopmental Disorders
- Genetic Neurodegenerative Diseases
- Plant Virus Research Studies
- Forensic and Genetic Research
- Animal Genetics and Reproduction
- Advanced Combinatorial Mathematics
- Plant Molecular Biology Research
- Algorithms and Data Compression
- Genetic and Environmental Crop Studies
- Nutrition, Genetics, and Disease
- Advanced Mathematical Theories and Applications
- Fungal and yeast genetics research
- Insect Resistance and Genetics
- Hearing Loss and Rehabilitation
- Genomics and Rare Diseases
University of Zagreb
2013-2024
Max Planck Institute for the Physics of Complex Systems
2013
Croatian Academy of Sciences and Arts
2012
Abstract During metaphase, forces on kinetochores are exerted by k-fibres, bundles of microtubules that end at the kinetochore. Interestingly, non-kinetochore have been observed between sister kinetochores, but their function is unknown. Here we show laser-cutting a k-fibre in HeLa and PtK1 cells bundle microtubules, which term ‘bridging fibre’, bridges k-fibres balances interkinetochore tension. We found PRC1 EB3 bridging fibre, suggesting it consists antiparallel dynamic microtubules. By...
The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety repeats unbounded length that can be arbitrarily distant in sequences as large human chromosomes. efficacy due the use complete set K-string ensemble which enables new method direct mapping symbolic DNA sequence into frequency domain, with straightforward identification peaks GRM diagram. In this way, we obtain very fast, efficient and highly automatized...
Much attention has been devoted to identifying genomic patterns underlying the evolution of human brain and its emergent advanced cognitive capabilities, which lie at heart differences distinguishing humans from chimpanzees, our closest living relatives. Here, we identify two particular intragene repeat structures noncoding DNA, spanning as much a hundred kilobases, that are present in genome but absent chimpanzee other nonhuman primates. Using novel computational method Global Repeat Map,...
Higher order repeats (HORs) containing tandems of primary and secondary repeat units (head-to-tail "tandem within tandem pattern"), referred to as regular HORs, are typical for primate alpha satellite DNAs most pronounced in human genome. Regular HORs known be a result recent evolutionary processes. In non-primate genomes mostly so called complex have been found, without head tail units. beetle Tribolium castaneum, considered model case genome studies, large identified, but no reported....
Previously it was found that the neuroblastoma breakpoint family ( NBPF ) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization these has been discovered by both methods, (HOR)-searching method HLS searching method. Using HOR with global map algorithm, here we identified tandemly organized HORs nonhuman primate NCBI reference genomes. We 50 canonical 3mer copies (Olduvai triplets), but none primates chimpanzee, gorilla,...
In fission yeast, microtubules push against the cell edge, thereby positioning nucleus in center. Kinesin-8 motors regulate microtubule catastrophe; however, their role nuclear is not known. Here we develop a physical model that describes how kinesin-8 affect centering by promoting catastrophe. Our predicts improved of presence motors, which confirmed experimentally living cells. The also characteristic time for recentering displaced nucleus, supported our experiments where using optical...
In this study, we investigated students’ understanding of concepts related to the microscopic model gas. We thoroughly reviewed relevant literature and conducted think alouds with students by asking them answer open-ended questions about kinetic molecular theory gases. Thereafter, transformed into multiple-choice questions, whereby distractors were based on results alouds. Thus, obtained a set 22 which constitutes our current version gases concept inventory. The inventory has been...
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee modern there a discontinuous jump from 0 50 tandemly organized HORs. Here we investigate structure of NBPF Neanderthal genome assembly Pääbo et al., comparing it results obtained for hg38.p14 chromosome 1. Our findings reveal corresponding HOR arrays...
In this article, we show that mono/oligonucleotide quadruplets, as basic structures of DNA, along with our classification trinucleotides, disclose an organization genomes based on purine-pyrimidine symmetry. Moreover, the structure and stability DNA are influenced by Watson-Crick pairing natural law creation conservation, according to which same mono- or oligonucleotide insertion must be inserted simultaneously into both strands DNA. Taken together, they lead quadruplets central mirror...
GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in centromeric region, it is increasing interest to efficient tools for computational identification and analysis HORs from known sequences.We develop a graphical user interface method, ColorHOR, given genomic sequence, without requiring priori information on composition sequence. ColorHOR...
Key string algorithm (KSA) could be viewed as robust computational generalization of restriction enzyme method. KSA enables and effective identification structural analyzes any given genomic sequences, like in the case NCBI assembly for human genome. We have developed a method, using total frequency distribution all r-bp key strings dependence on fragment length l, to determine exact size repeats within sequence, both monomeric HOR type. Subsequently, particular lengths equal each these...
Identification of approximate tandem repeats is an important task broad significance and still remains a challenging problem computational genomics. Often there no single best approach to periodicity detection combination different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used study primary periodicities in DNA sequences. Here we investigate application DFT method identify alphoid higher order repeats.We based on with mapping symbolic...
Abstract The centromere is important for segregation of chromosomes during cell division in eukaryotes. Its destabilization results chromosomal missegregation, aneuploidy, hallmarks cancers and birth defects. In primate genomes centromeres contain tandem repeats ~171 bp alpha satellite DNA, commonly organized into higher order (HORs). spite crucial importance, satellites have been understudied because gaps sequencing - genomic “black holes”. Bioinformatical studies sequences open...
Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension disorders therapeutic interventions. This study rigorously identified structurally analyzed alpha satellite higher-order repeats (HORs) within chromosome 15 in complete T2T-CHM13 assembly using high-precision GRM2023 algorithm. The most extensive HOR array reveals a novel cascading HOR, housing 429 15mer...
From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed precise alpha satellite higher-order repeat (HOR) structure using novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified HORs in centromere discovering a 59mer HOR—the longest HOR unit any primate to date. Additionally, it revealed first intertwined sequence three HORs, 18mer/27mer/45mer common...
AimTo precisely identify and analyze alpha-satellite higher-order repeats (HORs) in T2T-CHM13 assembly of human chromosome 3.MethodsFrom the recently sequenced complete 3, precise alpha satellite HOR structure was computed by using novel high-precision GRM2023 algorithm with global repeat map (GRM) monomer distance (MD) diagrams.ResultsThe major array 3 revealed a cascading HOR, housing 17mer copies subfragments periods 15 2. Within each row monomers were different types, but rows within...
Tandem repeats (TRs) are important components of eukaryotic genomes; they have both structural and functional roles: (i) form essential chromosome structures such as centromeres telomeres; (ii) modify chromatin structure affect transcription, resulting in altered gene expression protein abundance. There established links between variations TRs incompatibilities species, evolutionary development, mis-segregation, aging, cancer outcomes different diseases. Given the importance TRs, it seemed...