Everything you put in the research machine is gone for good: the challenge of this game is to survive with the limited resources you have available.
Here's a handy list of the current known resources and their availability:
- Grass: infinitely renewable resource, unless you pick up the Tuft with the shovel and feed it to the Science Machine;
- Saplings: same as the Grass;
- Reed: same as the Grass and the Saplings;
- Berries: these have a different behaviour, since many players use them for farming. A single bush can be harvested 5 times before going depleted, then you have to fertilize it. Feeding the bush to the Science machine completely destroys it with no possibility of going back;
- Manure: infinitely available, as long as you have a herd of beefalos near you, or a pigmen village;
- Beefalos: still unclear if they reproduce and at what rate.
- Pigmen: generated indefinitely from their village.
- Wood: trees can be planted back, unless you destroy the pine cones or burn the forest. Pro tip: dig up the tree stump to get one more log;
- Flint: limited. Those that you pick up don't respawn anywhere else;
- Rocks: limited. Destroying a boulder yields rocks and flint, but boulders don't respawn;
- Gold: limited. There's only a chance to get gold from mining a boulder and, as I already said, boulders don't respawn, BUT if you find a Pig King you can feed him meat or other items to get gold nuggets in return;
- Flowers & carrots: more research is needed. When you pick them you cannot replant them, but it looks like they can sponaneously appear in random spots of the map;
- Spiders: putting them in the resources because of the Silk. The nests generate new spiders when you kill them, up to their current limit (it should be 6 for the small nest, 9 for the medium and 12 for the big). Spider nests themselves can be "planted" with spider eggs, that are obtained when destroying a big nest (and maybe also from a medium nest);
- Rabbits: my guess here is that they're regenerated as long as their holes are intact (you can dig up a rabbit hole to force them out);
- Frogs: still unclear how they're generated;
- Fish: may be an infinite resource, but more research is needed;
- Turkeys: they're vermins and they're there to gobble on your berries! Randomly generated in any bush, you don't have to worry about their quantity.
As you can see, the list is still a work in progress, since I'm trying to discover everything on my own. I'll try to keep this updated everytime I'll find something new. Keep in mind anyway that Don't Starve is still in beta, so any of these informations is not fixed and still likely to be changed at any time.