Requires the Secretary to promulgate regulations that require each high- or medium- risk tier railroad carrier, public transportation operator, or over-the-road bus private operator to submit for approval by the Secretary: (1) an assessment of the vulnerability of the rail or public transportation system or over-the-road bus to terrorism; and (2) a security plan that addresses certain security performance requirements. Requires the Secretary to establish a security program for covered transportation not assigned to a high- or medium-risk tier.

Requires the Secretary to establish a program to make grants to state, local, and tribal governments, as well as infrastructure owners (including railroad carriers), public transportation agencies, and over-the-road bus operators for certain security improvements.

Makes grants to Amtrak for certain fire and life-safety improvements to tunnels on the Northeast Corridor.

Requires the Secretary to: (1) develop training programs to prepare railroad, public transportation, and over-the-road bus workers (including front-line employees) for potential threat conditions; and (2) establish a security exercises program for such workers and other named entities to respond to acts of terrorism.

Sets forth certain whistleblower protections for DHS, Department of Transportation (DOT), rail and public transportation, and over-the-road bus employees (including contractors and subcontractors) who have provided information or otherwise assisted in any investigation regarding certain conduct, or who have refused to violate or assist in the violation of any regulation related to national or homeland security.

Requires an increase in the number of DHS surface transportation security inspectors.

Requires implementation of a threat assessment screening program for, and a redress process for background checks done on, rail and public transportation and over-the-road bus employees (including contractors and subcontractors).

Sets forth civil penalties for violations of regulations and orders of the Secretary.

(Sec. 102) Requires the Secretary to assign each railroad carrier, public transportation operator, or over-the-road bus private operator (covered transportation) to a certain risk-based tier.

(Sec. 103) Directs the Secretary to issue regulations that: (1) require each provider of covered transportation assigned to a high- or medium-risk tier to assess their vulnerability to terrorism and to implement, subject to approval of the Secretary, a security plan that addresses certain security performance requirements; (2) establish standards for such assessments and plans; and (3) establish a security program for providers of covered transportation not assigned to a high- or medium-risk tier.

Imposes civil and criminal penalties for failure to comply with the requirements of this Act.

Requires the periodic review of vulnerability assessments and security plans by each provider of covered transportation.

Requires the Secretary to report to Congress on the feasibility of implementing named-based checks against terrorist watch lists for all National Railroad Passenger Corporation (Amtrak) passengers.

(Sec. 104) Directs the Secretary to develop, and submit to Congress, an information sharing plan to develop strategic intelligence on threats and vulnerabilities to covered transportation for dissemination to federal, state, and local agencies, tribal governments, and appropriate stakeholders.

(Sec. 105) Requires the Secretary to establish a program to make grants to providers of covered transportation with completed vulnerability assessments and approved security plans for certain security improvements. Authorizes appropriations for FY2008-FY2011.

(Sec. 108) Authorizes appropriations for FY2008-FY2011 to the Secretary to make grants to Amtrak for certain fire and life-safety improvements to tunnels on the Northeast Corridor.

(Sec. 109) Requires the Secretary to: (1) develop training programs to prepare covered transportation workers (including front-line employees) for potential threat conditions; and (2) establish a security exercises program for such workers and other named entities to respond to acts of terrorism. Requires each provider of covered transportation to: (1) develop, and submit for approval by the Secretary, a security training program; and (2) complete, not later than one year after approval, the training of all covered workers.

(Sec. 111) Requires the Secretary to carry out a research and development (R&D) program to improve the security of covered transportation. Authorizes appropriations for FY2008-FY2011.

(Sec. 112) Sets forth: (1) certain whistleblower protections for DHS, Department of Transportation (DOT), and covered transportation employees (including contractors and subcontractors) who have provided information or otherwise assisted in any investigation regarding certain conduct, or who have refused to violate or assist in the violation of any regulation, related to covered transportation security; and (2) criminal penalties for persons who violate such requirements. Directs the Attorney General to report annually to Congress on the enforcement of such requirements.

(Sec. 113) Directs the Secretary to increase the total number of full-time DHS surface transportation security inspectors to at least 600 by December 31, 2010.

(Sec. 114) Establishes in DHS a National Domestic Preparedness Consortium. Authorizes appropriations for FY2008-FY2011.

(Sec. 115) Authorizes the Secretary, acting through the Administrator of the Transportation Security Administration (TSA), to develop Visible Intermodal Protection Response (VIPR) teams to augment security for any mode of transportation at any location within the United States.

(Sec. 116) Establishes a National Transportation Security Center of Excellence at an institution of higher education to conduct research and education activities, and develop or provide professional security training (including training of rail and public transportation employees), with emphasis on the use of intelligent transportation systems, technologies, and architectures.

(Sec. 117) Provides that any statutory limitation on the number of TSA employees shall not apply to employees carrying out this Act.

(Sec. 118) Requires all security-related grants distributed under this Act to be administered on the basis of risk.

(Sec. 119) Directs the Secretary to implement a threat assessment screening program for covered transportation employees (including contractors and subcontractors).

(Sec. 120) Requires each provider of covered transportation to provide an adequate redress process for its employees (including contractors and subcontractors) who are adversely affected by background checks performed by the provider.

(Sec. 121) Establishes a task force to review lists of crimes that disqualify individuals from certain transportation-related employment under TSA regulations and to assess whether such lists are accurate indicators of a terrorism security risk.

(Sec. 122) Sets forth civil penalties for violations of regulations and orders of the Secretary.

(Sec. 123) Directs the Secretary to submit to Congress a threat assessment of a terrorist attack on the Nation's school bus transportation system.

(Sec. 124) Directs the Secretary to issue regulations to require certain enhanced security measures for shipments of security sensitive materials.

(Sec. 125) Directs the Secretary, acting through the Under Secretary for Science and Technology and the Director of the Domestic Nuclear Detection Office, to establish national voluntary consensus standards for the testing and use of technologies to improve the security of covered transportation. Directs the Secretary to utilize the Technology Clearinghouse to identify, acquire, and deploy technology and training for use by federal, state, local, and tribal agencies, emergency response providers, providers of covered transportation, shippers of hazardous materials, and others to prevent and respond to acts of terrorism on covered transportation.

(Sec. 126) Directs the Secretary and the Secretary of Transportation to jointly assess likely methods of deliberate attacks against rail tank cars used to transport toxic-inhalation-hazard materials, including the degree to which such methods may be successful in causing death, injury, or serious adverse effects to human health, the environment, or public welfare. Requires the Secretary to report to Congress on such assessment.

Requires the Secretary, acting through the National Infrastructure Simulation and Analysis Center, to conduct air dispersion modeling analysis of a release of such materials from a rail tank car in an urban area. Requires the Secretary to report to Congress detailing conclusions and findings with respect to such analysis.

(Sec. 127) Directs the Domestic Nuclear Detection Office to evaluate prototype systems (including spectroscopic technologies) to detect nuclear or radiological materials on the rails. Requires, upon completion of such evaluation, the Office, in coordination with Customs and Border Protection and the TSA, to ensure that certain protocols are established and a deployment strategy is developed to detect such materials arriving by rail. Requires, not later than September 30, 2008, the Office to report to Congress on such evaluation and strategy.

(Sec. 128) Requires recipients of grants for purchase of security plan technologies to give preference to qualified anti-terrorism technologies and technologies that are eligible for liability protections.

(Sec. 130) Requires the Secretary with respect to the screening of in-bound rail shipments to the United States for terrorists or weapons of mass destruction to: (1) deploy, where practicable, non-intrusive inspection imaging equipment at locations where rail shipments cross an international border to enter the United States; or (2) implement alternative procedures to screen such rail shipments at locations where deployment of such equipment is not practicable.

(Sec. 131) Directs the Secretary, in carrying out the threat assessment screening program for covered transportation employees (including contractors and subcontractors), to require high-risk tier providers of covered transportation to submit the names of their employees to the Secretary to conduct checks against terrorist watchlists and immigration status databases.

(Sec. 132) Directs the Comptroller General to conduct, and submit to Congress, an annual review regarding the administration and use of grants awarded under this Act.

(Sec. 133) Makes the Secretary the principal federal official responsible for transportation security. Delineates the roles and responsibilities of DHS and the Department of Transportation (DOT) in carrying out the requirements of this Act.

(Sec. 134) Directs the Secretary to assess, and report the results to Congress on, the safety and security vulnerabilities of placing high voltage electric transmission lines along active railroad rights-of-way.

(Sec. 135) Directs the Secretary to conduct a study of, and report to Congress on, foreign rail security practices, including the feasibility of implementing such practices in the United States.

(Sec. 136) Directs the Secretary of Transportation to establish a program to coordinate with state and local governments to minimize the need to transport toxic inhalation hazardous materials by rail.

(Sec. 137) Grants immunity from civil liability to persons who report threats to or acts of terrorism against transportation systems or passengers.

Title II: Secure Transportation Through Increased Use of Canine Detection Teams - (Sec. 201) Requires the Secretary to encourage, and coordinate with owners and providers of covered transportation to encourage, the deployment of canine detection teams at high-risk transportation systems at an increase of not less than ten percent of such teams at high-risk rail and mass transit systems for each fiscal year for FY2008-FY2012.

(Sec. 202) Authorizes the TSA's National Explosives Detection Canine Team Program to train up to an additional 100 canine detection teams per year, with at least a specified number of additional teams trained for each fiscal year for FY2008-FY2012. Requires detection teams to be deployed at covered transportation systems across the country. Directs the Administrator of TSA to report to Congress on personnel and resources needed to fulfill such requirements. Authorizes appropriations.

(Sec. 203) Requires the TSA Puppy Program to increase the number of domestically bred canines to meet the increase in demand for canine detection teams. Directs the Administrator of TSA to report to Congress on personnel and resources needed to fulfill such requirements. Authorizes appropriations.