This is not your father's recession, and it's not your typical recession, and the investment world has received yet another data point confirming the above.

Yale University, investors -- not a community college in Kansas, but Yale -- will lay-off as many as 300 employees as the economic downturn forces the Ivy League school to trim its operating budget, the Yale Daily News reported.

During times of economic distress, it's common for people to go back to school. But when it comes to MBA programs, things may be still be gloomy.

Bear in mind that these programs rely heavily on endowments. And when the investment market was bubbly, the returns were lush -- and so were the MBA programs.

Harvard reports that the value of its endowment has declined $8 billion between the end of June 2008 through October 2008. That would make Harvard's endowment worth 22% less than at the end of June, or $26.9 billion -- but it probably has further to fall thanks to illiquid assets like private equity interests. Meanwhile, Harvard and its peers could be in trouble because fewer people will be able to afford college given the market crash. That will mean college administrators are facing some tough choices.

Harvard is responding to the decline in its endowment by taking a "hard look" at staffing levels and compensation. It is forecasting a 30% drop for its endowment ending in June 2009, which would bring it to $25.8 billion, down another $1 billion. While this strikes me as optimistic, it does suggest the extent of the damage and the challenges Harvard and its peers face.

The options for universities are dwindling. A study suggests that tuition has risen 439% since 1982 while median family incomes have increased only 137% during that period. If tuition continues to rise at that rate, few families will be able to afford college. With the student loan market in dire straits and incomes likely to fall further due to layoffs, the only way for colleges to attract top students who can't pay will be to cut tuition even more on the lower income families while making up the difference by raising tuition for the wealthiest ones.

Harvard is an easy target for the woes of our economy. Its business school produced George W. Bush, the fellow who's presided over the current economic catastrophe, and Rick Wagoner, the CEO of the largest automobile maker who's led its stock down 95% in the last eight years and now wants $25 billion worth of taxpayer money to keep the millions rolling into his bank account. But Harvard had these folks for just two years, so it's tough to blame the school for the current predicament.

However, with $36.9 billion in assets (as of June 30), Harvard also has the largest endowment of any university. And thanks to its big exposure to very illiquid interests in venture capital (VC) and private equity (PE) firms, Harvard leads a growing list of limited partners (LPs) which are selling stocks and those very illiquid interests in order to come up with the cash needed to fulfill their capital calls to these partnerships.

This requires some explaining. VC firms raise money from limited partners such as wealthy individuals, foundations, pension funds, and endowments. But the LPs don't write checks up front -- instead they hold onto their cash and must write a check when the VC calls and asks for the money when the VC is on the verge of making an investment. The problem for many LPs like Harvard is that much of their stock portfolio is locked up in hedge funds and these illiquid VC and PE interests.

Your 401(k) and ROTH IRA might be down, and shares of student lender Sallie Mae (NYSE: SLM) have gone from $50 to $15 since October, over concerns about the student loan market.

But you'll be happy to know that the endowment for Harvard is chugging right along, up in the 7-9% range for its fiscal year ended in June, according to The Wall Street Journal (subscription required).

In the current market malaise, that's enough to make it the best-performing major endowment, according to experts. That's especially impressive given the fund's massive size: $35 billion.

The Journal reports that "The endowment's staff pursued a strategy of shielding the fund from market downturns by purchasing credit-default swaps that helped protect it from wild market swings. Harvard also had a larger position than many endowments in plain-vanilla Treasury debt, which outperformed the stock market."

I have just one question: With a $35 billion endowment growing at 7% per year, why do they need to charge $45 thousand per yeah? To its credit, the school announced late last year that it would extend much more generous financial aid to middle-class families.

The sub-prime mortgage market is in shambles. But Wall Street, making every effort to rid itself of risky mortgage-backed securities, has found a new group of potential buyers -- university endowments.

The Wall Street Journal reported (subscription required) that university endowments have started to dip into the risky world of buying sub-prime mortgage debt. An opportunity recently stemmed from two money-losing hedge funds at Bear Stearns (NYSE: BSC), and one that required loans from various banks to halt the seizure of the fund. Merrill Lynch & Co. (NYSE: MER) a lender to these funds, auctioned some assets it had seized from Bear for $850 million. However, the auction sold for less than half that amount, according to people familiar with the matter.

Lou Morrell, vice president for investments and treasurer at Wake Forest University in Winston-Salem, N.C. is quoted as saying he sees value in those auctions. "There's an opportunity out there to buy these loans at a discount," he told the WSJ, and that "will be popular with a lot of endowments out there." The university is placing $25 million of its $1.2 billion endowment with a hedge fund to invest in sub-prime mortgages.

They're not the only ones dealing in big risk either.

Harvard, Stanford, Notre Dame, and MIT have all received permission from the IRS to allow donors to invest in their endowments (WSJ, registration required). By structuring investments as charitable trusts, donors receive a regular distribution until death, and then the money goes to the school.

The returns earned by endowments at schools such as Harvard and Yale are impressive. The Harvard endowment has returned 15.2% per year for the past 10 years, crushing the S&P 500's return of 8.3%. In addition to their strong performance, endowments are diversified across so many different asset classes that they often bear a very low correlation to the stock market. While investing in endowments is often inefficient in terms of taxes, the historically higher returns some have earned has more than made up for it.

If tax rules loosen up and allow endowment investors to keep a greater share of their gains, we could see endowments become a popular vehicle for retirement planning. Instead of watching the Final Four basketball games, investors could keep a close eye on which school is earning the highest returns.

I wonder how much correlation there would be between the prestige of a school and the performance of its endowment. As Warren Buffett has said, "Success in investing doesn't correlate with IQ once you're above the level of 25. Once you have ordinary intelligence, what you need is the temperament to control the urges that get other people into trouble in investing."