Čo je život a ako ho študovať...

Prednáška 4Čo je život a ako ho študovať III.

Opportunity na Marse

Biologické systémy fungujú podľa pravidiel termodynamiky

ΔG = ΔH – TΔS

Zmena voľnej energie je vo vzťahu k zmene entalpie a entropie


Druhý zákon termodynamiky: v uzavretom systéme dochádza k zvyšovaniu neusporiadanosti a k znižovaniu voľnej (využiteľnej) energie

Voľná energia

Entropia

Sadava a kol. (2007). Life: The Science of Biology. Sinnauer Ass.

Ako je potom možné, že sú živé systémy usporiadané?

Biologické systémy fungujú podľa pravidiel termodynamikyV prípade endotermických procesov, pri ktorých je ΔG > 0 je potrebný prísun energie sú reakcie spriahnuté s exotermickými reakciami


Voľn

á en

ergi

a

Smer reakcie

Voľn

á en

ergi

aVoľn

á en

ergi

a

reaktanty

Tranzičný stav

Ea

ΔG

produkty

Chemické reakcie v živých organizmoch sú urýchľované katalyzátormi


ΔG0 = -RT ln[Y]/[X]

100% glukózo-1-P 95% glukózo-6-P 5% glukózo-1-P


Živé organizmy sú otvorené chemické systémy mimo rovnováhy


4. Život na Zemi je kontinuálny (abiogenéza vs. biogenéza)

Louis Pasteur(1822–1895)1859

Spoločné charakteristiky živých foriem na Zemi

ZÁVER: Živé organizmy vznikajú zo živých organizmov

rast mikroorgamizmov

VÝSLEDKY

žiadny rast

4. Život na Zemi je kontinuálnySpoločné charakteristiky živých foriem na Zemi

molekuly

bunky

tkanivá

orgány

organizmy

populácie

ekosystémy

biosféra

komunity

hypotéza Gaia(J. Lovelock)http://www.nature.com/nature/videoarchive/lovelock/

5. Život je hierarchizovanýSpoločné charakteristiky živých foriem na Zemi

6. Život je založený na dynamických interakciáchSpoločné charakteristiky živých foriem na Zemi


Dictyostelium discoideum –jednoduchý model bunkovej diferenciácie

agregácia „slimák“

„Stonka“„Stonka“

↓Živiny

https://www.youtube.com/watch?v=5h8WOWEqP6o

Produkcia „autoinduktora“

Indukcia odpovede susedov

Špecifická odpoveď bunkovej populácie

Koordinované správanie buniek u Dictyostelium discoideum

AGREGÁCIA

Negative feedback

Positive feedback

Feedforward relay

Inhibitory crosstalk

Stimulatory crosstalk

Komponenty živých systémov sú zostavené do sietí, v rámci ktorých medzi sebou interagujú

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5

10

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20

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0 9 11 13 15 18 22 25

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cAM

P (p

mol

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prot

eínu

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Vďaka týmto interakciám vykazujú živé systémy tzv. emergentné správanie, t.j. správanie, ktoré nie je možné dedukovať z vlastností individuálnych komponentov

Konc

entrá

cia

chem

ické

ho a

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ora

D

C

B

A

c d

a b

g

f

e

Barabási, A.L. (2002). Linked. Perseus Publishing. (V pavučine sítí, 2005, Paseka)

Leonhard Euler a problém mostov v Královci

Robustnosť a SIEŤOVANIE

Biologické systémy sú reprezentované sieťami interakcií

6. Biologické adaptácie sú výsledkom evolúcie prostredníctvom prírodného výberu

Spoločné charakteristiky živých foriem na Zemi


Current Biology 24, 2156–2160, September 22, 2014 ª2014 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2014.07.059

ReportArcherfish Actively Controlthe Hydrodynamics of Their Jets

Peggy Gerullis1 and Stefan Schuster1,*1Department of Animal Physiology, University of Bayreuth,95440 Bayreuth, Germany

Summary

Among tool-using animals [1–4], none are known to adap-tively change the hydrodynamic properties of a free jet of wa-ter—a task considered difficult in human technology [5–7].Hunting archerfish can strike their targets with preciselyaimed water jets (e.g., [8, 9]), but they are also presentlythought to be unable to actively control the hydrodynamicsof their jets [8–13]. By using specifically trained fish, wewere able to monitor several aspects of jet production andpropagation as the fish fired at targets over a much widerrange of distances than previously explored [10, 13]. Weshow that jets that have to travel farther also live longer.Furthermore, the time needed until water assembles at thejet tip is not fixed. Rather, it is adjusted so that maximumfocusing occurs just before impact. Surprisingly, the fishachieve this by modulating the dynamics of changes in thecross-section of their mouth opening, a mechanism thatseems to not have been applied yet in human-built nozzles.The timing adjustments archerfish make in order to power-fully hit targets over an extended range strikingly parallelthe situation in the ‘‘uniquely human’’ ability of powerfulthrowing [14–18]. Based on the key role throwing played inhuman encephalization and cognitive evolution [14–20],skillfully ‘‘throwing’’ water should similarly have led to thecorrelated rapid evolution of cognitive skills in this animal.

Results and Discussion

In the field, archerfish can deliver powerful blows to targetsfrom more than 2 m distance (Movie S1 available online). Abrief powerful impact, needed to overcome prey attachment[10], could result if water that is released last catches up withthe tip [13]. Water has been found to be indeed ‘‘assembled’’at the tip [13] in jets aimed at very close targets (10 cm), result-ing in a force at impact that is comparable to forces measuredat 30 cm height [10]. Hence, a simple scenario could explainhow the fish hit prey with sufficient power throughout theirlarge hunting range: a speed gradient in the jet causes the wa-ter to be focused at the jet tip after about 10 cm. The focusedmass then travels upward, ready to hit any prey item in its path.We report here that this simple view is wrong and that instead,the fish adjust the distance at which water is maximallyfocused.

Specifically trained archerfish allowed us to monitor severalaspects of jet formation and propagation over a far wider rangeof preset target distances than previously examined. Thetrained fish fired accurate shots at targets presented at20 cm, 40 cm, and 60 cm height above the water’s surface,assuming defined position and orientation in each of theirshots and tolerating the strong illumination needed for

accurate high-speed recordings. In contrast to the scenariodescribed above, assembling of water at the tip is not gener-ally finished after 10 cm of travel. In jets fired at targets at60 cm height (Figures 1A and 1B), the jet tip was not completedeven after 30 cm of travel (Figure 1A) and was focused onlymuch later, before impact (Figure 1B). The difference in shapebetween the traveling ‘‘midway’’ and the ‘‘preimpact’’ jets is sorobust that it is easy to sort them out in a collection of images(Figure S1).Jets fired at close-range targets were fully focused much

earlier. A jet aimed at 20 cm height is focused at that height(Figure 1D), but a jet aimed at a target at 60 cm height is not(Figure 1A). However, jet tips recorded just before impactwere equally well focused, and their shapes bore no informa-tion on how long they had traveled before (Figures 1C and1D). To test this notion, we made use of the ease with whichhuman pattern vision can reliably detect differences in thecomplex structure of the jets (Figure S1). Twelve neutralobservers were asked to group a collection of 21 pictures ofpreimpact jet tips (seven for each target height) into three clas-ses. Despite considerable effort, the observers grouped theimages completely at random, with no relation to target height(p = 0.98, c2 test; see Experimental Procedures). Hence, imme-diately before impact, jets were equally well focused, regard-less of target height.En route views of the traveling jets revealed a further range-

dependent difference in the stability of the jets. Figure 1E illus-trates this with images of the shaft of the jets (see Figure S1)after a common path of 30 cm. The jets aimed at more distanttargets showed fewer modulations (Rayleigh instabilities,[21, 22]) in diameter, allowing human observers to groupthem in accordance with target height (p < 0.001, c2 test; n =30 images, 15 at each height, grouped by each of N = 8observers). Rare cases in which a jet had just missed theclose-range target (at 20 cm height) and disintegrated withoutinteracting with the target (see Experimental Procedures) wereparticularly instructive. When mixing en route views (obtainedafter 30 cm of travel) of the shaft of jets that were aimed at thethree different target distances, human observers could stillreadily predict target height even when they did not knowhow many examples belonged to each class (p < 0.001, c2

test; n = 7 images of jets, n = 17 images of jets, and n = 21 im-ages of jets after 30 cm travel distance but aimed at 20 cm,40 cm, and 60 cm height, respectively; N = 14 observers).Are the target-range adjustments reflected in the way the

jets are formed? Tip speed increased systematically in all ar-cherfish jets, tightly following (Figures 2A–2C; R2 > 0.99 in allcases) an empirical relation of the general form

vtipðtÞ=vmax 2Dv expð2 t=tÞ: (Equation 1)

Here, vmax denotes the hypothetical maximum speed the tipwould obtain (if water continued to flow out forever), Dv is thetotal increment in speed (from when the jet tip leaves themouth to vmax), and t is the time constant of the increase intip speed. In our analysis of 313 jets (Figure 2), the ranges ofthe three parameters were 5.8–6.8 ms21 (vmax), 2.7–3.8 ms21

(Dv), and 6.6–20.0 ms (t). Note that an increase in speed istypical for unsteady jets [21]. In contrast to a projectile firedfrom a gun, even a jet that rises against gravity can speed up*Correspondence: [email protected]

https://www.youtube.com/watch?v=S4G_MeUUZlI http://www.bbc.com/news/science-environment-29046018

as long as the tip is connected with water that flows out withincreasing speed. Most remarkably, the profile of increase inspeed depended on target height (nonlinear mixed effectsmodel: p < 0.001; Figures 2A–2C; Table S1 and Figure S2; totalwater volume is independent of height [10]). Both fish system-atically raised the speed increment Dv with target height (p <0.001; Figure 2D) and thus adjusted the difference in speed be-tweenwater released first andwater released last according totarget height.

The general pattern of increase in speed at the tip (Equation1) does not also determine the stability of the jets. Figures 2Eand 2F show jets mimicked with syringes that either stayedcoherent while water left the syringe or broke up before all wa-ter had left the syringe. Despite their very different stability,they did not significantly differ in the time course of speed in-crease at their tips (Figures 2E and 2F; difference in vmax, Dv,and t: p > 0.05 in each case). The truemastery of the fish there-fore seems to be covarying the stability and the initial speedprofile of their jets. To shoot, archerfish rapidly compress theirgill covers, forcing water out from a ‘‘gun barrel’’ whose upperhalf is a ridge in the roof of their mouth and whose bottom half

is formed by the hardened surface of their tongue [10–12] (Fig-ure S3). Water does not leave this gun barrel directly into theair, but it leaves after passage of an enlargement. A similararrangement reduces the production of satellite drops in themammalian penis [23] and may have a similar stabilizing func-tion for archerfish jets.Given the apparent rigidity of the shooting apparatus, we

first looked for chemical ways by which the fish could controlthe hydrodynamics of their jets. Dynamic viscosity h and sur-face tension s affect the so-called Ohnesorge number

Oh=h=ðLrsÞ1=2; (Equation 2)

which determines the stability of a free jet [5] formed with acharacteristic length L from a fluid with density r. It is well es-tablished that even the presence of small traces of chemicalscan strongly affect this number [24] so that the fish could chem-ically adjust their jets by adding more or less substances to it.We therefore analyzed the surface tension and the shearing-rate dependence of viscosity directly in the water that the fishhad fired. However, surface tension in these samples was

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A C

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Figure 1. Focus Distance and Instability ofArcherfish Jets Are Not Fixed but Depend onTarget Distance

Trained archerfish allowed us to monitor severalaspects of their jet production, from formation un-til impact, as they engaged targets (black dots) at20 cm, 40 cm, or 60 cm height above water level.(A and B) Examples of jets fired at a target at60 cm height. Although water has assembled atthe tip before impact (B), this has not yet fullyoccurred after 30 cm of travel (A) (see also Fig-ure S1).(C) Areasmarked blue and red schematically indi-cate preimpact and en route phases of jets,respectively, shown in (D) and (E).(D) Examples (from 39 recordings) of preimpactjet tips (1 cm before impact) showing that water

can be focused much earlier, depending on target height. Preimpact focusing is equally well at all height levels, and images of preimpact tip contain noinformation on how far the jet had traveled before (p = 0.98; c2 test).(E) In addition to when the tip forms, stability of main shaft of jet differs, depending on target height. Examples of jets (from 83 recordings) observed after acommon distance of 30 cm (schematically depicted at 30 cm height) contain information on target distance (p < 0.001; c2 test).

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Figure 2. Archerfish Adjust the SpeedGradient ofTheir Jets According to Target Height

(A–C) Depiction of how speed at jet tip followedthe general relation vtip(t) = vmax 2 Dv exp(2t/t)(vmax, maximum speed; Dv, speed increment; t,time constant) at each target height (20 cm,40 cm, and 60 cm). Time course of tip speed dur-ing first 20 ms for shots fired by fish 2 is shown(see Figure S2 for fish 1). Points are averages of41, 57, and 44 speed measurements (all fits inA–C, R2 > 0.99).(D) Speed increment Dv significantly increasedwhen jets were launched toward higher targets(mean 6 5% confidence intervals for fish 1[filled-in bar] and fish 2 [open bar]; all differencesp < 0.001).(E and F) The time course of tip speed does notgenerally predict stability. Mimicking the archer-fish’s pattern of increase in tip speed can leadto stable (E) or unstable (F) jets (see examples ininsets).

Archerfish Shape Their Jets2157

Current Biology 24, 2156–2160, September 22, 2014 ª2014 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2014.07.059

ReportArcherfish Actively Controlthe Hydrodynamics of Their Jets

Peggy Gerullis1 and Stefan Schuster1,*1Department of Animal Physiology, University of Bayreuth,95440 Bayreuth, Germany

Summary

Among tool-using animals [1–4], none are known to adap-tively change the hydrodynamic properties of a free jet of wa-ter—a task considered difficult in human technology [5–7].Hunting archerfish can strike their targets with preciselyaimed water jets (e.g., [8, 9]), but they are also presentlythought to be unable to actively control the hydrodynamicsof their jets [8–13]. By using specifically trained fish, wewere able to monitor several aspects of jet production andpropagation as the fish fired at targets over a much widerrange of distances than previously explored [10, 13]. Weshow that jets that have to travel farther also live longer.Furthermore, the time needed until water assembles at thejet tip is not fixed. Rather, it is adjusted so that maximumfocusing occurs just before impact. Surprisingly, the fishachieve this by modulating the dynamics of changes in thecross-section of their mouth opening, a mechanism thatseems to not have been applied yet in human-built nozzles.The timing adjustments archerfish make in order to power-fully hit targets over an extended range strikingly parallelthe situation in the ‘‘uniquely human’’ ability of powerfulthrowing [14–18]. Based on the key role throwing played inhuman encephalization and cognitive evolution [14–20],skillfully ‘‘throwing’’ water should similarly have led to thecorrelated rapid evolution of cognitive skills in this animal.

Results and Discussion

In the field, archerfish can deliver powerful blows to targetsfrom more than 2 m distance (Movie S1 available online). Abrief powerful impact, needed to overcome prey attachment[10], could result if water that is released last catches up withthe tip [13]. Water has been found to be indeed ‘‘assembled’’at the tip [13] in jets aimed at very close targets (10 cm), result-ing in a force at impact that is comparable to forces measuredat 30 cm height [10]. Hence, a simple scenario could explainhow the fish hit prey with sufficient power throughout theirlarge hunting range: a speed gradient in the jet causes the wa-ter to be focused at the jet tip after about 10 cm. The focusedmass then travels upward, ready to hit any prey item in its path.We report here that this simple view is wrong and that instead,the fish adjust the distance at which water is maximallyfocused.

Specifically trained archerfish allowed us to monitor severalaspects of jet formation and propagation over a far wider rangeof preset target distances than previously examined. Thetrained fish fired accurate shots at targets presented at20 cm, 40 cm, and 60 cm height above the water’s surface,assuming defined position and orientation in each of theirshots and tolerating the strong illumination needed for

accurate high-speed recordings. In contrast to the scenariodescribed above, assembling of water at the tip is not gener-ally finished after 10 cm of travel. In jets fired at targets at60 cm height (Figures 1A and 1B), the jet tip was not completedeven after 30 cm of travel (Figure 1A) and was focused onlymuch later, before impact (Figure 1B). The difference in shapebetween the traveling ‘‘midway’’ and the ‘‘preimpact’’ jets is sorobust that it is easy to sort them out in a collection of images(Figure S1).Jets fired at close-range targets were fully focused much

earlier. A jet aimed at 20 cm height is focused at that height(Figure 1D), but a jet aimed at a target at 60 cm height is not(Figure 1A). However, jet tips recorded just before impactwere equally well focused, and their shapes bore no informa-tion on how long they had traveled before (Figures 1C and1D). To test this notion, we made use of the ease with whichhuman pattern vision can reliably detect differences in thecomplex structure of the jets (Figure S1). Twelve neutralobservers were asked to group a collection of 21 pictures ofpreimpact jet tips (seven for each target height) into three clas-ses. Despite considerable effort, the observers grouped theimages completely at random, with no relation to target height(p = 0.98, c2 test; see Experimental Procedures). Hence, imme-diately before impact, jets were equally well focused, regard-less of target height.En route views of the traveling jets revealed a further range-

dependent difference in the stability of the jets. Figure 1E illus-trates this with images of the shaft of the jets (see Figure S1)after a common path of 30 cm. The jets aimed at more distanttargets showed fewer modulations (Rayleigh instabilities,[21, 22]) in diameter, allowing human observers to groupthem in accordance with target height (p < 0.001, c2 test; n =30 images, 15 at each height, grouped by each of N = 8observers). Rare cases in which a jet had just missed theclose-range target (at 20 cm height) and disintegrated withoutinteracting with the target (see Experimental Procedures) wereparticularly instructive. When mixing en route views (obtainedafter 30 cm of travel) of the shaft of jets that were aimed at thethree different target distances, human observers could stillreadily predict target height even when they did not knowhow many examples belonged to each class (p < 0.001, c2

test; n = 7 images of jets, n = 17 images of jets, and n = 21 im-ages of jets after 30 cm travel distance but aimed at 20 cm,40 cm, and 60 cm height, respectively; N = 14 observers).Are the target-range adjustments reflected in the way the

jets are formed? Tip speed increased systematically in all ar-cherfish jets, tightly following (Figures 2A–2C; R2 > 0.99 in allcases) an empirical relation of the general form

vtipðtÞ=vmax 2Dv expð2 t=tÞ: (Equation 1)

Here, vmax denotes the hypothetical maximum speed the tipwould obtain (if water continued to flow out forever), Dv is thetotal increment in speed (from when the jet tip leaves themouth to vmax), and t is the time constant of the increase intip speed. In our analysis of 313 jets (Figure 2), the ranges ofthe three parameters were 5.8–6.8 ms21 (vmax), 2.7–3.8 ms21

(Dv), and 6.6–20.0 ms (t). Note that an increase in speed istypical for unsteady jets [21]. In contrast to a projectile firedfrom a gun, even a jet that rises against gravity can speed up*Correspondence: [email protected]

Charakteristiky životaObchádzanie dizorganizácieUsporiadanosť Každá štruktúra/aktivita je v špecifickom vzťahu s inou

štruktúrou/aktivitouAdaptácia Špecifické štruktúry a správanie umožňuje organizmu

prežívať v danom prostredíMetabolizmus Siete chemických reakcií umožňujúcich premenu energie,

a jej využitie na dôležité životné funkcieAktívny pohyb Využitie vlastných síl organizmu na pohyb v danom

prostredíDráždivosť Schopnosť organizmu detegovať signály v prostredí a

reagovať na ne

Reprodukcia Schopnosť organizmu produkovať nové jedince toho istého typu

Ontogenéza, vývin Usporiadaná séria progresívnych zmien vedúcich k zvýšenému stupňu komplexnosti (zložitosti)

Gény Organizmy majú k dispozícii jednotky dedičnosti, ktoré kontrolujú ich vlastnosti

Evolúcia Počas evolúcie získavajú organizmy nové spôsoby prežívania a reprodukcie v danom prostredí

Pokračovanie skupiny napriek smrti jednotlivcov

Ako je možné experimentálne študovať komplikované biologické fenomény?

Redukcia komplikovaného problému na jednoduché otázky je predpokladom pre pochopenie zložitých fenoménov

REDUKCIONIZMUS VS HOLIZMUS

Najefektívnejší spôsob štúdia biologického fenoménu je študovať ho v najjednoduchšom biologickom systéme, u ktorého bol identifikovaný

DELBRÜCKOV PRINCÍP

Jednoduché organizmy ako model pre štúdium zložitých biologických fenoménov

KVASINKY (Saccharomyces cerevisiae):Základy bioenergetikyPrincípy biogenézy bunkových organelPrincípy regulácie bunkového cykluPaul Nurse, Leland Hartwell, Nobelova cena (2001)

HMYZ (Drosophila melanogaster):Chromozómový základ dedičnostiPrincípy ontogenézy (vývinu)Princípy behaviorálnej genetikyThomas Morgan, Nobelova cena (1933)Christiane Nüsslein-Volhard, Nobelova cena (1995)

BAKTERIOFÁGY:Základy molekulárnej genetikyMax Delbrück, Nobelova cena (1969)

Princípy vezikulárneho transportu v bunkáchRandy Schekman, Nobelova cena (2013)


ČERVY (Caeonorhabditis elegans):Princípy vývinovej biológieZáklady programovanej bunkovej smrtiGenetický základ starnutiaSydney Brenner, Robert Horwitz, John Sulston, Nobelova cena (2002)

MÄKKÝŠE (Aplysia):Základy neurobiológieEric Kandel, Nobelova cena (2000)

OBOJŽIVELNÍKY (Xenopus laevis):Základy vývinovej biológieHans Speman, Nobelova cena (1935)Tim Hunt, Nobelova cena (2001)

http://www.dailymotion.com/video/xjhxzw_memory-research-aplysia-californica-memorable-snail_school


Arabidopsis thaliana

•  Krátky životný cyklus (6 týždňov)

•  Relatívne malý genóm (125 miliónov párov báz)

•  Možnosť ľahkej genetickej manipulácie

•  ...


Danio rerio


Mus musculus

Heterocephalus glaber, Naked mole-rat, krtkopotkan holý

Extrémna dĺžka života: 30 rokov (myš 4 roky)Rezistencia k onkologickým transformáciámBunky H. glaber vykazujú fenomén skorej kontaktnej inhibície in vitro(ECI, early contact inhibition)

Štúdium modelových organizmov môže byť dôležité pre klinickú medicínu

Bunky H. glaber sekretujú vysokomulekulárny hyaluronan

Tian et al. (2013). Nature 499: 346-349.

HA, hylarunonan

HAase, hyaluronidaseHAS, HA synthaseNMR, naked mole rat; GP, guinea pig; M, mouse; H, human; SF, skin fibroblasts

Čo určuje naše správanie? Základné princípy genetiky správania boli odvodené zo štúdia modelových organizmov

Dvorenie samčeka u Drosophila melanogaster

Fruitless (FRU): Kontrolór pohlavnej identity nervového systému Drosophila melanogaster

fruitless samčekovia sú bisexuálni, v spoločnosti samčekov tvoria „retiazky“ (courtship chains)

Dvorenie drozofíl je pod genetickou kontrolou

Demir, E., Dickson, B.J. (2005) Cell 121, 785-794

Agresívne správanie drozofíl ako model pre genetiku správania človeka

Chen, S. a kol. (2002) Proc. Natl. Acad. Sci. USA 99, 5664-5668

Výstraha krídlami Šermovanie

Boxovanie Obranné gesto porazeného

Experimentálna komôrka

Nilsen, S. P. a kol. (2004). Proc. Natl. Acad. Sci. USA 101, 12342-12347Yurkovic, A. a kol. (2006). Proc. Natl. Acad. Sci. USA 103, 17519-17524

Vzorce agresívneho správania sa odlišujú medzi samcami a samičkami D. melanogaster

Bojové techniky špecifické pre samcov: Boxovanie, „Tussling“ Bojové techniky špecifické pre samičky: „Head-butting“

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