Under Construction

Techniques in the Baram Lab are goal and project-driven and span molecular biology to systems to behavior.


A partial list:

  • Single cell resolution ISH/ICC
  • ChIP & ChIP-seq,
  • RNA-Seq & single cell transcriptomics (with Ali Mortazavi)
  • Viral genetic (AAV) tract tracing
  • Tracts manipulation using chemogenetic and optogenetic approaches
  • Brain clearing- too many variants….
  • Live two-photon imaging of microglia/ Neuron interactions
  • In vivo and ex vivo MR Imaging
  • Battery of memory tests
  • Battery of please/reward tests



The Lab has created a useful model of early-life adversity/ stress that has been widely and successfully adopted worldwide. We get numerous requests for info on how to set this paradigm called the Limited Bedding and Nesting (LBN) cages. So, here are a few resources: These include a rationale, a protocol, a few references and what you need to buy to set it up (easy).


Brief rationale:

As is the case in humans, maternal care plays a critical role in rodent brain development. Beyond simply providing nutrition and safety in the nest, the dam is critical for providing important sensory signals and relaying environmental cues to the pups. These sensory signals may contribute to the proper maturation and pruning of synapses in developing emotional and cognitive brain circuits. It follows that perturbation of dam-pup interactions is a potent way to manipulate the early-life environment, provoke stress and disrupt brain circuit maturation.

We provoke chronic, persistent changes in maternal nurturing behaviors by the use of cages with limited nesting and bedding material (Gilles et al, 1996; Molet et al, 2014; Naninck et al, 2015). This ‘simulated poverty’ induces stress in the dams (Ivy et al, 2008), and alters their behaviors (Ivy et al, 2008; Rice et al, 2008; Rincón-Cortés and Sullivan, 2014). This latter approach has provoked chronic unremitting stress in the pups (Gilles et al,1996; Ivy et al,2008; Rice et al,2008; Moriceau et al,2009; Raineki et al, 2010; Wang et al,2011; Molet et al, 2014; Naninck et al, 2015). Notably, there is little evidence of physical stress of the pups, with no hypothermia (Bolton 2018). Thus, the chronic stress, including plasma corticosterone elevation and adrenal hypertrophy (Gilles et al, 1996; Rice et al, 2008) seems to be a direct result of the fragmented, unpredictable sensory signals from the mothers (Moriceau et al 2009; Baram et al, 2012; Molet et al, 2014; Molet et al,2016). Though signs of stress dissipate rapidly when dams and pups are returned to routine cages, the LBN experience promotes protean consequences on cognitive and emotional brain networks and on functional outcomes.


Protocol: Setting up the limited bedding/nesting chronic early-life stress (CES) paradigm in rats and mice.

Day Procedure Note
Time-pregnancy Order time-pregnant females from your animal supplier or arrange to breed females in-house.

To limit the effects of previous experience on the dam’s maternal behavior and response to stress, always use virgin naïve females in rats, and make sure they are not juvenile.


Minimize disturbances and other stress sources throughout pregnancy.

Check for births at least twice daily on the days surrounding expected parturition; at least two dams will give birth within the same 10–12 hour period to mix the pups across litters on the day of manipulation.







Postnatal day 2
























Prepare limited bedding and nesting cages:

Start with clean, empty standard housing cages.

Position a fine-gauge, plastic coated aluminum mesh platform to sit approximately 2.5 cm above the cage floor. Folding edges of mesh along the length approximately 3 cm so that platform sits above the bottom of the cage, permitting droppings to fall below the platform without trapping the pups.

Cover cage floor with a small amount of standard bedding. This should not reach the top of the mesh.

Provide a limited amount of nesting material. For rats, add one-half of a single paper towel to the cage. For mice, add one-half of a single NESTLET square (Ancare, Bellmore, NY).


Limited bedding/nesting manipulation:

To minimize genetic factors, pups from several dams are mixed and matched and assigned to CES or control dams at random.


For each litter, quickly and gently remove all pups from the home cage; identify the sex of each pup (using anogenital distance) and place males and females into separate, euthermic holding cages.

Repeat for each litter, keeping separate holding cages for male and female pups. Once all litters are removed and sorted, randomly assign dams to the control or limited bedding/nesting conditions.


Place dam into fresh, clean standard cage (with normal amounts of bedding and nesting material). Randomly transfer pups from the male and female holding cages to control cage with the dam.

Limited bedding/nesting cages: Place dam into the cage with mesh platform and limited bedding and nesting material. Randomly transfer pups from the male and female holding cages to the experimental cage with the dam.



Plastic-coated mesh dimensions: 0.4 × 0.9 cm. McNichols Co.,  catalog no. 4700313244.








Be careful the separation time is limited to under 15–20 minutes.


Litter size: because it influences both pup weight and hence maturation of the brain, as well as maternal behaviors per pup, we typically have 4 – 6 pups per mouse litter and 10 – 12 per rat litter.  sex ratio should be approximately 1:1.

Counter-balance the order in which you replace pups with the dams between control and limited bedding/nesting conditions to limit differences in the total duration pups are separated.

Postnatal day 2 to postnatal day 9 Leave control and limited bedding/nesting cages undisturbed (and unchanged) until postnatal day 9.


Observe maternal behavior during that period at least twice daily, as described in Ivy et al., 2008. Alternatively, video behavior. Consider looking at continuous behaviors and patterns of care over 60-90 minutes
Postnatal day 10 In the morning, change all cages (control and limited bedding/nesting) to fresh, standard cages with normal bedding and nesting material.


Return cages to standard husbandry and changing schedules.



Refs, links:








What you need:

Order the plastic coated mesh from McNichols Co.; the updated catalog number in the 2014 paper is #4700313244

http://www.mcnichols.com/product/4700313244?navCode=cc:std#) if the link doesn’t take you directly there just search for the catalogue number on their website.