Updated from 12:25 p.m. EDT

On a flat to positive day for health stocks Wednesday, several companies declared breakups, acquisitions, patent rulings and approvals.

RNAi therapeutic company Alnylam ( ALNY) and Merck ( MRK) said Wednesday that they mutually agreed to terminate their July 2006 amended-and-restated collaboration agreement.

Merck agreed in October 2006 to pay $1.1 billion for Sirna (siRNA) Therapeutics, an Alnylam competitor that develops RNAi technology. Alnylam said Wednesday that it rescinded all grants of its intellectual property related to current and future Merck development programs, including former co-development programs. The company maintained guidance that it will have $435 million in cash by the end of the year.

Alnylam shares closed up $1.28, or 4.1%, to $32.40. Merck closed up 99 cents, or 2%, to $51.56.

Not everyone was breaking up. Allergan ( AGN - Get Report) announced a $370 million all-cash deal to acquire privately held Esprit Pharma, which markets Sanctura for overactive bladder. The Food and Drug Administration recently granted approval for an extended-release version of the drug. Allergan shares rose 82 cents, or 1.3%, to close at $63.03.

Related to that acquisition, Indevus Pharmaceuticals ( IDEV - Get Report), which licensed Sanctura to Esprit, said Wednesday that it amended its license, commercialization and supply agreement with Allergan. Indevus shares slid 43 cents, or 5.9%, to close at $6.85.

Elsewhere, biotechnology company Neuralstem ( CUR - Get Report) said the U.S. Patent and Trademark Office ruled in its favor in a patent dispute with StemCells ( STEM).

After a re-examination, the patent office issued an official rejection of each of the claims in the four patents that StemCells brought against Neuralstem in its lawsuit, according to a Neuralstem press release Wednesday. StemCells fell 5 cents, or 2.4%, to $2.04, and Neuralstem closed down 3 cents, or 1%, at $3.

Other companies gave clinical and regulatory updates.

Alexza Pharmaceuticals ( ALXA) was moving in the other direction. The company said after market close on Tuesday that it expects to begin the first of two 300-patient phase III trials for iAZ-004 for acute agitation in patients with schizophrenia or bipolar disorder, late in the first quarter of 2008.

AZ-004 is being developed through Symphony Allegro, a product development collaboration formed between Alexza and Symphony Capital. Alexza shares gained 45 cents, or 5.3%, to $8.97, helping the Nasdaq biotechnology index, which was up 2.38, or 0.3%, to 847.90.

And on the approval side, the FDA said it cleared the FluMist nasal spray influenza vaccine for children between the ages of two and five. FluMist is made by MedImmune, which was recently acquired by AstraZeneca ( AZN - Get Report).

AstraZeneca said MedImmune anticipates shipping FluMist with the expanded label to health care providers in the coming days so that vaccinations may be offered to eligible individuals ahead of and throughout the upcoming influenza season. AstraZeneca edged up 21 cents, or 0.4%, to $48.21.