Assessing somatic hypermutation in Ramos B cells after overexpression or knockdown of specific genes

B cells start their life with low affinity antibodies generated by V(D)J recombination. However, upon detecting a pathogen, the variable (V) region of an immunoglobulin (Ig) gene is mutated approximately 100,000-fold more than the rest of the genome through somatic hypermutation (SHM), resulting in high affinity antibodies. In addition, class switch recombination (CSR) produces antibodies with different effector functions depending on the kind of immune response that is needed for a particular pathogen. Both CSR and SHM are initiated by activation-induced cytidine deaminase (AID), which deaminates cytosine residues in DNA to produce uracils. These uracils are processed by error-prone forms of repair pathways, eventually leading to mutations and recombination. Our current understanding of the molecular details of SHM and CSR come from a combination of studies in mice, primary cells, cell lines, and cell-free experiments. Mouse models remain the gold standard with genetic knockouts showing critical roles for many repair factors (e.g. Ung, Msh2, Msh6, Exo1, and polymerase η). However, not all genes are amenable for knockout studies. For example, knockouts of several double-strand break repair proteins are embryonically lethal or impair B-cell development. Moreover, sometimes the specific function of a protein in SHM or CSR may be masked by more global defects caused by the knockout. In addition, since experiments in mice can be lengthy, altering expression of individual genes in cell lines has become an increasingly popular first step to identifying and characterizing candidate genes. Ramos - a Burkitt lymphoma cell line that constitutively undergoes SHM - has been a popular cell-line model to study SHM. One advantage of Ramos cells is that they have a built-in convenient semi-quantitative measure of SHM. Wild type cells express IgM and, as they pick up mutations, some of the mutations knock out IgM expression. Therefore, assaying IgM loss by fluorescence-activated cell scanning (FACS) provides a quick read-out for the level of SHM. A more quantitative measurement of SHM can be obtained by directly sequencing the antibody genes. Since Ramos cells are difficult to transfect, we produce stable derivatives that have increased or lowered expression of an individual gene by infecting cells with retroviral or lentiviral constructs that contain either an overexpression cassette or a short hairpin RNA (shRNA), respectively. Here, we describe how we infect Ramos cells and then use these cells to investigate the role of specific genes on SHM (Figure 1).     

Dipeptidyl peptidase III: a multifaceted oligopeptide N-end cutter

Dipeptidyl peptidase III (DPP III), the sole member and representative of the M49 family of metallopeptidases, is a zinc-dependent aminopeptidase. It sequentially hydrolyses dipeptides from the N-terminal of oligopeptides ranging from three to 10 amino acid residues. Although implicated in an array of pathophysiological phenomena, the precise function of this peptidase is still unclear. However, a number of studies advocate its contribution in terminal stages of protein turnover. Altered expression of DPP III which suggests its involvement in primary ovarian carcinoma, oxidative stress (Nrf2 nuclear localization), pain, inflammation and cataractogenesis has recently led to resurgence of interest in delineating the role of the peptidase in these pathophysiological processes. This review article intends to bring forth the latest updates in this arena which may serve as a base for future studies on the peptidase.     

Observations on parturition and allomothering in wild capped langur (Trachypithecus pileatus)

A birth during the day by a capped langur (Trachypithecus pileatus Blyth, 1843) was recorded at Pakhui Wildlife Sanctuary, Arunachal Pradesh, India. The birth took 43 min. Allomothering was observed 3 h after the birth. An average of 9% of daily active time was shared by four allomothers (three adults, one subadult) during the first 15 days of the infants life. Total time allomothering was proportional to the age of the allomothers (241 min for oldest; 214 min for youngest).     

A fundamental approach for the estimation of the mechanical glass transition temperature in gelatin

The paper constitutes an attempt to overcome the empiricism prevalent in the estimation of the glass transition temperature (Tg) of gelatin networks using rheological techniques. In doing so, it presents a study of the viscoelastic properties of a well-characterised gelatin sample covering the structural properties from the rubbery region to the glassy state. The pattern of oscillatory behaviour on shear is given by a master curve produced by shifting data obtained at different temperatures along the logarithmic time scale. Data reduction does not hold for all temperatures thus giving rise to thermorheological complexity. Within the temperature range at which molecular processes are represented by a simple distribution of relaxation times, a fundamental argument is developed to pinpoint the mechanical Tg. This should improve confidence in measured glassy properties over the empirical indicators found in the literature. As a demonstration, the glass transition temperature of gelatin at "zero moisture" obtained using the proposed framework of analysis is contrasted with earlier attempts to identify the mechanical Tg of gelatin solids.     

Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene

Respiratory syncytial virus (RSV) infection is one of the major causes of respiratory tract infection for which no vaccine or antiviral treatment is available. The RSV NS1 protein seems to antagonize the host interferon (IFN) response; however, its mechanism is unknown. Here, we used a plasmid-borne small interfering RNA targeting the NS1 gene (siNS1) to examine the role of NS1 in modulating RSV infection. RSV replication was reduced in A549 cells, but not IFN-deficient Vero cells, transfected with siNS1. siNS1 induced upregulated expression of IFN-beta and IFN-inducible genes in A549 cells. siNS1-transfected human dendritic cells, upon RSV infection, produced elevated type-1 IFN and induced differentiation of naive CD4+ T cells to T helper type 1 (TH1) cells. Mice treated intranasally with siNS1 nanoparticles before or after infection with RSV showed substantially decreased virus titers in the lung and decreased inflammation and airway reactivity compared to controls. Thus, siNS1 nanoparticles may provide an effective inhibition of RSV infection in humans.     

Females with paired occurrence of cancers in the UADT and genital region have a higher frequency of either Glutathione S-transferase M1/T1 null genotype

Upper Aero digestive Tract (UADT) is the commonest site for the development of second cancer in females after primary cervical cancer. Glutathione S-transferase (GSTM1 and / or T1) null genotype modulates the risk of developing UADT cancer (primary as well as second cancer). The aim of this study was to evaluate the difference in GST null genotype frequencies in females with paired cancers in the UADT and genital region as compared to females with paired cancers in the UADT and non-genital region. Forty-nine females with a cancer in the UADT and another cancer (at all sites-genital and non-genital) were identified from a database of patients with multiple primary neoplasms and were analyzed for the GSTM1 and T1 genotype in addition to known factors such as age, tobacco habits, alcohol habits and family history of cancer. Frequencies of GSTM1 null, GSTT1 null, and either GSTM1/T1 null were higher in females with paired occurrence of cancer in the UADT and genital site (54%, 33% and 75% respectively) in comparison to females with paired occurrence of cancer in the UADT and non-genital sites (22%, 6% and 24% respectively). The significantly higher inherited frequency of either GSTM1/T1 null genotype in females with a paired occurrence of cancers in UADT and genital region (p = 0.01), suggests that these females are more susceptible to damage by carcinogens as compared to females who have UADT cancers in association with cancers at non-genital sites.     

Role of cell surface heparan sulfate proteoglycans in endothelial cell migration and mechanotransduction

Endothelial cell (EC) migration is critical in wound healing and angiogenesis. Fluid shear stress due to blood flow plays an important role in EC migration. However, the role of EC surface heparan sulfate proteoglycans (HSPGs) in EC adhesion, migration, and mechanotransduction is not well understood. Here, we investigated the effects of HSPG disruption on the adhesion, migration, and mechanotransduction of ECs cultured on fibronectin. We showed that disruption of HSPGs with heparinase decreased EC adhesion rate by 40% and adhesion strength by 33%. At the molecular level, HSPG disruption decreased stress fibers and the size of focal adhesions (FAs), increased filopodia formation, and enhanced EC migration. Under flow condition, heparinase treatment increased EC migration speed, but inhibited shear stress-induced directionality of EC migration and the recruitment of phosphorylated focal adhesion kinase in the flow direction, suggesting that HSPGs are important for sensing the direction of shear stress. In addition, decreasing cell adhesion by lowering fibronectin density enhanced EC migration under static and flow condition, but did not affect the directional migration of ECs under flow. Based on our results, we propose that HSPGs play dual roles as mechanotransducer on the EC surface: (1) HSPGs-matrix interaction on the abluminal surface regulates EC migration speed through an adhesion-dependent manner, and (2) HSPGs without binding to matrix (e.g., on the luminal surface) are involved in sensing the direction of flow through an adhesion-independent manner.     

AID and Igh switch region-Myc chromosomal translocations

Chromosomal translocations involving Ig heavy chain switch regions and an oncogene, like Myc, represent early initiating events in the development of many B cell malignancies. These translocations are widely believed to result from aberrant class switch recombination (CSR). Recent reports have produced conflicting models for the role of activation-induced cytidine deaminase (AID) in this process. Here, we discuss possible roles of AID, CSR, and somatic hypermutation in generating chromosomal translocations and in tumor progression.