The barcoding of life

Barkodiranje povezuje taksonomiju, molekularnu filogenetiku i populacijsku genetiku. Dokazana je mogućnost kreiranja baze podataka za životinje na temelju COI sekvence. Za druga carstva potrebno je provesti opsežnije analize u svrhu pronalaska najpogodnijeg barkoda. Daljnji razvoj i napredak ovog projekta omogućit će jasniji uvid u bioraznolikost, a analize su puno objektivnije nego kod klasičnih morfoloških analiza. Zanimljivo je i pomisliti na postojanje online enciklopedije života na Zemlji. Iako je projekt zapravo relativno nov, svakodnevno se ulaže trud da se premoste eventualne prepreke u procesima izgradnje ovakvog sustava. Metode u molekularnoj biologiji postaju jeftinije i mogu se uvesti u postupak barkodiranja. Razvijaju se mnoge nove metode poput pirosekvenciranja koje omogućava brzu analizu pomiješanih uzoraka. Već postoje i razvijene tehnike nedestruktivne ekstrakcije DNA iz nedavno prikupljenih uzoraka, što pospješuje njihovu konzervaciju. Sve prepreke moraju biti jasno definirane i premošćene da bi se BOLD baza podataka mogla u potpunosti uspješno razviti. Ukoliko neka organizacija poput Global Biodiversity Information Facility ili All Species Foundation preuzme ovaj projekt, to bi bio veliki korak prema dugovječnosti koja nedostaje mnogim dosadašnjim bazama podataka. Zaključno, vrijeme je da se današnje društvo suoči sa mnogim biološkim problemima kao što su izbjegavanje pandemija, očuvanje bioraznolikosti, pružanje biološke sigurnosti te zaštita vrsta.Barcoding associates taxonomy, molecular phylogenetics and population genetics. It demonstrates the possibility of creating a database of the animals on the basis of COI sequences. For other kingdoms of life it is necessary to conduct a more comprehensive analysis in order to find the most appropriate barcode. Further development and progress of this project will provide a clearer insight into the biodiversity, and analysis are much more objective than conventional morphological analysis. It is interesting to think of the existence of the online encyclopedia of life on Earth. Although the project is actually relatively novel, daily efforts are made to overcome any obstacles in the process of building this system. Methods in molecular biology are becoming cheaper and can be introduced into the process of barcoding. Development of many new methods such as pyrosequencing will allow rapid analysis of mixed samples. Techniques of nondestructive extraction of DNA from the recently collected samples are already developed, which promotes conservation of samples. All obstacles must be clearly defined and overridden so that BOLD database could develop fully and successfully. If an organization such as the Global Biodiversity Information Facility or All Species Foundation acquire this project, it would be a major step toward longevity lacking many current databases. Finally, it is time to confront today's society with many biological problems such as avoiding pandemics, biodiversity conservation, providing security and protection of biological species

The barcoding of life

Barkodiranje povezuje taksonomiju, molekularnu filogenetiku i populacijsku genetiku. Dokazana je mogućnost kreiranja baze podataka za životinje na temelju COI sekvence. Za druga carstva potrebno je provesti opsežnije analize u svrhu pronalaska najpogodnijeg barkoda. Daljnji razvoj i napredak ovog projekta omogućit će jasniji uvid u bioraznolikost, a analize su puno objektivnije nego kod klasičnih morfoloških analiza. Zanimljivo je i pomisliti na postojanje online enciklopedije života na Zemlji. Iako je projekt zapravo relativno nov, svakodnevno se ulaže trud da se premoste eventualne prepreke u procesima izgradnje ovakvog sustava. Metode u molekularnoj biologiji postaju jeftinije i mogu se uvesti u postupak barkodiranja. Razvijaju se mnoge nove metode poput pirosekvenciranja koje omogućava brzu analizu pomiješanih uzoraka. Već postoje i razvijene tehnike nedestruktivne ekstrakcije DNA iz nedavno prikupljenih uzoraka, što pospješuje njihovu konzervaciju. Sve prepreke moraju biti jasno definirane i premošćene da bi se BOLD baza podataka mogla u potpunosti uspješno razviti. Ukoliko neka organizacija poput Global Biodiversity Information Facility ili All Species Foundation preuzme ovaj projekt, to bi bio veliki korak prema dugovječnosti koja nedostaje mnogim dosadašnjim bazama podataka. Zaključno, vrijeme je da se današnje društvo suoči sa mnogim biološkim problemima kao što su izbjegavanje pandemija, očuvanje bioraznolikosti, pružanje biološke sigurnosti te zaštita vrsta.Barcoding associates taxonomy, molecular phylogenetics and population genetics. It demonstrates the possibility of creating a database of the animals on the basis of COI sequences. For other kingdoms of life it is necessary to conduct a more comprehensive analysis in order to find the most appropriate barcode. Further development and progress of this project will provide a clearer insight into the biodiversity, and analysis are much more objective than conventional morphological analysis. It is interesting to think of the existence of the online encyclopedia of life on Earth. Although the project is actually relatively novel, daily efforts are made to overcome any obstacles in the process of building this system. Methods in molecular biology are becoming cheaper and can be introduced into the process of barcoding. Development of many new methods such as pyrosequencing will allow rapid analysis of mixed samples. Techniques of nondestructive extraction of DNA from the recently collected samples are already developed, which promotes conservation of samples. All obstacles must be clearly defined and overridden so that BOLD database could develop fully and successfully. If an organization such as the Global Biodiversity Information Facility or All Species Foundation acquire this project, it would be a major step toward longevity lacking many current databases. Finally, it is time to confront today's society with many biological problems such as avoiding pandemics, biodiversity conservation, providing security and protection of biological species

Analysis of metaphase spindle mechanics in HeLa cells by laser microsurgery

Glavna struktura koja upravlja procesom je diobeno vreteno, a jedna od klasa mikrotubula u toj strukturi su kinetohorna vlakna koja vežu kromosome putem kinetohora na centromeri. Trenutne spoznaje govore da dva sestrinska kinetohorna vlakna nisu u međusobnoj izravnoj interakciji. U ovom radu pažnja je usmjerena na opisivanje nove klase mikrotubula u vretenu a nazvana je premošćujući mikrotubuli. Ta nova klasa tvori vlakna antiparalelnih mikrotubula i lateralno povezuje sestrinska kinetohorna vlakna te sudjeluje u mehanici diobenog vretena. U provedenom istraživanju korišten je konfokalni mikroskop za snimanje živih stanica HeLa te je korištena laserska mikrodisekcija vanjskog kinetohornog vlakna, da bi se pokazala prisutnost premošćujućih mikrotubula te ispitala njihova uloga u distribuciji sila u vretenu. Ove su rezultate potvrdili eksperimenti sa stanicama sa smanjenom razinom proteina PRC1 koji je sastavni dio metafaznog vretena. Procesi u regiji između sestrinskih kromosoma analizirani su u stanicama s obilježenim proteinom EB3, uključenim u rast mikrotubula na + kraju. U oba eksperimenta potvrđena je prisutnost kompresivne sile i sile tenzije u metafaznom diobenom vretenu.Main structure that orchestrates mitosis is the mitotic spindle, and one of the microtubule classes comprised within are the kinetochore fibers, which bind to chromosomes via kinetochores on the centromere. It is currently believed that there is no direct interaction between two sister kinetochore fibers. The focus of this research is to describe a novel class of microtubules in the spindle, which was named bridging microtubules. This new class forms antiparallel bundles, laterally connects sister kinetochore fibers and contributes to spindle mechanics. In conducted research, confocal microscope was used for live-cell imaging of HeLa, and the laser microsurgery was applied on outermost kinetochore fiber in order to confirm bridging microtubule presence and to test their function in force distribution in the spindle. By using cells with decreased level of PRC1 protein, protein involved in metaphase spindle mechanics, we showed that bridging bundle contributes to force balance in the spindle. Microtubule dynamics in the region between sister kinetochores was also analyzed in cells with labeled EB3 protein involved in the growth of microtubule 's + end. Laser microsurgery confirmed compressive and tensile force in the metaphase spindle in both experiments

The barcoding of life

Barkodiranje povezuje taksonomiju, molekularnu filogenetiku i populacijsku genetiku. Dokazana je mogućnost kreiranja baze podataka za životinje na temelju COI sekvence. Za druga carstva potrebno je provesti opsežnije analize u svrhu pronalaska najpogodnijeg barkoda. Daljnji razvoj i napredak ovog projekta omogućit će jasniji uvid u bioraznolikost, a analize su puno objektivnije nego kod klasičnih morfoloških analiza. Zanimljivo je i pomisliti na postojanje online enciklopedije života na Zemlji. Iako je projekt zapravo relativno nov, svakodnevno se ulaže trud da se premoste eventualne prepreke u procesima izgradnje ovakvog sustava. Metode u molekularnoj biologiji postaju jeftinije i mogu se uvesti u postupak barkodiranja. Razvijaju se mnoge nove metode poput pirosekvenciranja koje omogućava brzu analizu pomiješanih uzoraka. Već postoje i razvijene tehnike nedestruktivne ekstrakcije DNA iz nedavno prikupljenih uzoraka, što pospješuje njihovu konzervaciju. Sve prepreke moraju biti jasno definirane i premošćene da bi se BOLD baza podataka mogla u potpunosti uspješno razviti. Ukoliko neka organizacija poput Global Biodiversity Information Facility ili All Species Foundation preuzme ovaj projekt, to bi bio veliki korak prema dugovječnosti koja nedostaje mnogim dosadašnjim bazama podataka. Zaključno, vrijeme je da se današnje društvo suoči sa mnogim biološkim problemima kao što su izbjegavanje pandemija, očuvanje bioraznolikosti, pružanje biološke sigurnosti te zaštita vrsta.Barcoding associates taxonomy, molecular phylogenetics and population genetics. It demonstrates the possibility of creating a database of the animals on the basis of COI sequences. For other kingdoms of life it is necessary to conduct a more comprehensive analysis in order to find the most appropriate barcode. Further development and progress of this project will provide a clearer insight into the biodiversity, and analysis are much more objective than conventional morphological analysis. It is interesting to think of the existence of the online encyclopedia of life on Earth. Although the project is actually relatively novel, daily efforts are made to overcome any obstacles in the process of building this system. Methods in molecular biology are becoming cheaper and can be introduced into the process of barcoding. Development of many new methods such as pyrosequencing will allow rapid analysis of mixed samples. Techniques of nondestructive extraction of DNA from the recently collected samples are already developed, which promotes conservation of samples. All obstacles must be clearly defined and overridden so that BOLD database could develop fully and successfully. If an organization such as the Global Biodiversity Information Facility or All Species Foundation acquire this project, it would be a major step toward longevity lacking many current databases. Finally, it is time to confront today's society with many biological problems such as avoiding pandemics, biodiversity conservation, providing security and protection of biological species

Analysis of metaphase spindle mechanics in HeLa cells by laser microsurgery

Glavna struktura koja upravlja procesom je diobeno vreteno, a jedna od klasa mikrotubula u toj strukturi su kinetohorna vlakna koja vežu kromosome putem kinetohora na centromeri. Trenutne spoznaje govore da dva sestrinska kinetohorna vlakna nisu u međusobnoj izravnoj interakciji. U ovom radu pažnja je usmjerena na opisivanje nove klase mikrotubula u vretenu a nazvana je premošćujući mikrotubuli. Ta nova klasa tvori vlakna antiparalelnih mikrotubula i lateralno povezuje sestrinska kinetohorna vlakna te sudjeluje u mehanici diobenog vretena. U provedenom istraživanju korišten je konfokalni mikroskop za snimanje živih stanica HeLa te je korištena laserska mikrodisekcija vanjskog kinetohornog vlakna, da bi se pokazala prisutnost premošćujućih mikrotubula te ispitala njihova uloga u distribuciji sila u vretenu. Ove su rezultate potvrdili eksperimenti sa stanicama sa smanjenom razinom proteina PRC1 koji je sastavni dio metafaznog vretena. Procesi u regiji između sestrinskih kromosoma analizirani su u stanicama s obilježenim proteinom EB3, uključenim u rast mikrotubula na + kraju. U oba eksperimenta potvrđena je prisutnost kompresivne sile i sile tenzije u metafaznom diobenom vretenu.Main structure that orchestrates mitosis is the mitotic spindle, and one of the microtubule classes comprised within are the kinetochore fibers, which bind to chromosomes via kinetochores on the centromere. It is currently believed that there is no direct interaction between two sister kinetochore fibers. The focus of this research is to describe a novel class of microtubules in the spindle, which was named bridging microtubules. This new class forms antiparallel bundles, laterally connects sister kinetochore fibers and contributes to spindle mechanics. In conducted research, confocal microscope was used for live-cell imaging of HeLa, and the laser microsurgery was applied on outermost kinetochore fiber in order to confirm bridging microtubule presence and to test their function in force distribution in the spindle. By using cells with decreased level of PRC1 protein, protein involved in metaphase spindle mechanics, we showed that bridging bundle contributes to force balance in the spindle. Microtubule dynamics in the region between sister kinetochores was also analyzed in cells with labeled EB3 protein involved in the growth of microtubule 's + end. Laser microsurgery confirmed compressive and tensile force in the metaphase spindle in both experiments

PRC1‐labeled microtubule bundles and kinetochore pairs show one‐to‐one association in metaphase

In the mitotic spindle, kinetochore microtubules form k‐fibers, whereas overlap or interpolar microtubules form antiparallel arrays containing the cross‐linker protein regulator of cytokinesis 1 (PRC1). We have recently shown that an overlap bundle, termed bridging fiber, links outermost sister k‐fibers. However, the relationship between overlap bundles and k‐fibers throughout the spindle remained unknown. Here, we show that in a metaphase spindle more than 90% of overlap bundles act as a bridge between sister k‐fibers. We found that the number of PRC1‐GFP‐labeled bundles per spindle is nearly the same as the number of kinetochore pairs. Live‐cell imaging revealed that kinetochore movement in the equatorial plane of the spindle is highly correlated with the movement of the coupled PRC1‐GFP‐labeled fiber, whereas the correlation with other fibers decreases with increasing distance. Analysis of endogenous PRC1 localization confirmed the results obtained with PRC1‐GFP. PRC1 knockdown reduced the bridging fiber thickness and interkinetochore distance throughout the spindle, suggesting a function of PRC1 in bridging microtubule organization and force balance in the metaphase spindle

Lieb-Robinson Bounds for Harmonic and Anharmonic Lattice Systems

We prove Lieb-Robinson bounds for the dynamics of systems with an infinite dimensional Hilbert space and generated by unbounded Hamiltonians. In particular, we consider quantum harmonic and certain anharmonic lattice systems

Hidden genetic diversity of ‘Candidatus Phytoplasma solani’ strains in Istrian vineyards: how small can be rich

Grapevine Yellows (GY) are economically important diseases associated to phytoplasmas (genus ‘Candidatus Phytoplasma’), uncultivable bacteria from the class Mollicutes. In Euro-mediterranean region, GY are mainly attributed to phytoplasmas belonging to ribosomal 16SrXII-A subgroup ('Ca. P. solani'; Bois Noir phytoplasma; BNp) and 16SrV group (flavescence dorée phytoplasma; FDp), with the latter one being a quarantine pathogen (Plavec et al. 2015, Quaglino et al. 2013). Although symptomatology can be similar, epidemiology of FDp and BNp is very different as they are transmitted by different insect vectors and could have different alternative hosts. In Croatia, GY diseases have been continuously monitored since 1997 with FDp appearing only in 2009 (Šeruga Musić et al. 2011). While BNp is more diverse and widespread, FDp belonging to 3 map phylogenetic clusters are differently distributed throughout regions. Istria is heavily affected with FDp since 2014 with only one genotype (mapFD2/M54) being attributed to great losses (Plavec et al. 2019). On the contrary, information on BNp diversity is scarce with only couple of genotypes detected so far (Plavec et al, manuscript in preparation). Therefore, the aim of this case study was to assess the diversity of BNp genotypes in a small selected area of Istria, in order to draw attention to the presence and importance of BNp as GY agent in this important Croatian viticultural region

Effective Rheology of Bubbles Moving in a Capillary Tube

We calculate the average volumetric flux versus pressure drop of bubbles moving in a single capillary tube with varying diameter, finding a square-root relation from mapping the flow equations onto that of a driven overdamped pendulum. The calculation is based on a derivation of the equation of motion of a bubble train from considering the capillary forces and the entropy production associated with the viscous flow. We also calculate the configurational probability of the positions of the bubbles.Comment: 4 pages, 1 figur