Referee 2's Review:

This manuscript reports some interesting and important results that are relevant to understanding the pathogenesis of malaria during pregnancy, a major health problem globally. The expression of P. falciparum genes among isolates from pregnant women and non-pregnant donors, and parasites lines selected for pregnancy malaria phenotypes were evaluated by comparison to the expression by the P. falciparum reference line 3D7. One candidate gene in particular that was expressed at higher levels in placental parasites was further studied (Pfl1785w).

Overall, this is a worthwhile manuscript that reports results that will be of significant interest to the scientific community. However, there are a number of important issues that I feel need to be addressed in the manuscript.

Major Comments:
The presentation and description of the study and results needs revision. In parts it is hard to follow exactly what was done, and what controls and samples were used in the different experiments.
Furthermore, this is compounded by the use of the terms like 'PAM parasites' and 'PAM phenotype', or 'non-PAM'. It is unclear at times what isolates the authors are referring to. It would be much clearer to use specific terms for relevant parasites (especially in the results section). Eg. placental isolates, CSA-selected lines, BeWo-selected lines, children's isolates, etc

Controlling for differences in the developmental stages of different parasites is a critical issue and needs to be further described and discussed - it would be important to highlight the limitations of the approaches used in the discussion. This is not an easy issue to address in performing studies on human samples, and studies of this type are essential. However, it is still important to discuss the limitations and be open about them. Specific issues in this regard include:
- Placental isolate pools were compared to 3D7 pools - was a separate 3D7 pool made for each of the placental pools to match the developmental stages? (page 4)
- Page 6 and Fig 3 - what were the stages of the different parasite isolates used compared to the reference line? Any differences should be discussed. How do we know whether the differences shown in Fig 3 are statistically significant?

Antibodies to Pfl1785w - more details needed on the serum used, especially age and infection status. This important because other differences between the men and women studied could explain the differences in antibody reactivity.

Var2csa was the only var gene found to be up-regulated in placental parasites. Its unlikely that a 3D7 array would adequately detect other upregulated var genes because sequence diversity would preclude hybridization of var cDNA to the 3D7 var probes. This limitation should be mentioned.

It would be very helpful if the authors could expand on the comparison between their results and those of the Seattle group reported by Fried et al 2007, and Francis et al 2007. Interestingly, Fried et al reported that var2csa was also expressed in some children's isolates, and another recent paper reported antibodies to CSA-adherent parasites among children.

Other comments:

Title - I suggest the word 'novel' is removed since many of the genes have already been identified in another recent study.

Introduction - please provide references for the statement 'Plasma
inhibitory activity to iE binding CSA is not dependent on the geographical origin of parasites or plasma'

Page 9 - the paragraph starting with 'Further work to.....' is not clear and needs re-wording

There is an error in the labeling and order of figures and figure legends (see Fig 4 and 5, p22).

Abstract - the statement 'was specifically recognized by serum samples from P. falciparum-exposed pregnant women' is not entirely correct, since many men also had antibodies....median antibody reactivity was higher for pregnant women.

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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.