The second case, which made headlines around the world, was the 10-year prison sentence for Xiyue Wang, a Princeton post-graduate history student who was in Iran doing research for a doctoral thesis on late 19th Century and early 20th Century history.
Wang "digitally archived" 4,500 pages of Iranian documents for foreign research institutions, according to Mizan Online.
It was unclear how long Wang has been in Iranian custody.
The US State Department did not identify its jailed citizen, but accused Iran of fabricating national security-related charges to detain Americans and foreigners.
The State Department also reacted strongly and called for immediate release of all USA citizens in jails in Iran.
Mohseni-Eje'i said Wang entered the country "through a special connection but the ministry of intelligence identified him and arrested him".
Kotkin said it is common for researchers traveling to multiple sites to photocopy or scan documents they do not have time to go through in each country, so they can "rush on to their next place of research". While remaining US sanctions have slowed economic gains promised by the accord, signs that global interest in Iran is growing have disturbed some hardliners, who foresee their power waning. Wang is one of several Americans held by Iran.
Xiyue Wang had been arrested last August, with a spokesman for the Iranian state judiciary announcing on Sunday that the sentence had been handed down. The Iran nuclear deal, negotiated under the Obama administration, has not been met with favor under President Trump's administration.
Iran has arrested numerous journalists, businesspeople, and academics - typically with Iranian-American citizenship - visiting the country on similar charges.
"We were very distressed to learn that charges were brought against him in connection with his scholarly work, and to learn of the subsequent conviction and sentence", said Princeton spokesman Daniel Day.
The conservative-dominated judiciary has clashed with Mr Rouhani, who has sought to ease social restrictions and release political prisoners.
The arrest of the president's brother, meanwhile, stunned many in Iran. He was not previously known to be among the handful of Americans detained in Iran.
The Washington Post names other Americans in Iranian custody, including art-gallery manager Karan Vafadari; businessman Siamak Namazi and his 81-year-old father Baquer; and Nizar Zakka, an Internet freedom activist who is a US permanent resident from Lebanon.