Context based mixture model for cell phase identification in automated fluorescence microscopy

Background  

Automated identification of cell cycle phases of individual live cells in a large population captured via automated fluorescence microscopy technique is important for cancer drug discovery and cell cycle studies. Time-lapse fluorescence microscopy images provide an important method to study the cell cycle process under different conditions of perturbation. Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task.     

Gelling interactions of phycocolloids extracted from red algae with a galactomannan from locust bean and a glucomannan from konjac tuber

The synergistic interaction between three red algae extracts and the galactomannan from locust bean (Ceratonia siliqua L.) and the glucomannan from the konjac tuber (Amorphophallus konjac C. Koch (syn.A. rivieri Durien var. konjac (C. Kock) Engler)) has been characterized in terms of gel properties. The extract obtained fromEucheuma alvarezii Doty (E. cottonii of commerce) was highly synergistic with bothkonjac flour and locust bean gum.Furcellaria fastigiata (Huds.) Lamour andEucheuma gelatinae (Esper) extracts were only slightly synergistic with locust bean gum, but were found to be highly synergistic with konjac flour.     

Conidium differentiation in Aspergillus nidulans wild-type and wet-white (wetA) mutant strains

Conidium (asexual spore) differentiation in wild-type and the wet-white (wetA) mutant of Aspergillus nidulans was compared in intact chains of successively older conidia. Carbohydrate cytochemistry helped define three stages (Stages I, II, and III) of wild-type conidium maturation on the basis of changes in the ultrastructure and composition of the conidium wall. Conidia of the wetA6 mutant strain formed normally but failed to mature during Stages II and III. Specifically, the inner wall layer of wetA6 conidia did not condense during Stage II and two wall layers that stained for carbohydrates did not form during the transition to Stage III. Concomitantly, wetA6 conidia formed large cytoplasmic vacuoles and underwent lysis. The wetA gene appears to have a conidium-specific function for the modification of the conidium wall during Stages II and III. These modifications of the conidium wall are essential for the stability of mature, dormant conidia.     

The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection

Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust protection against autologous intra-vaginal simian-human immunodeficiency virus (SHIV) challenge that was predicted by high serum nAb titers. Here, we show that nAb in these protected RM targeted a glycan hole proximal to residue 465 in gp120 in all cases. nAb also targeted another glycan hole at residues 241/289 and an epitope in V1 at varying frequencies. Non-neutralizing antibodies directed at N611-shielded epitopes in gp41 were also present but were more prevalent in RM with low nAb titers. Longitudinal analysis demonstrated that nAb broadened in some RM during sequential immunization but remained focused in others, the latter being associated with increases in nAb titer. Thirty-eight monoclonal antibodies (mAbs) isolated from a protected RM with an exceptionally high serum neutralization titer bound to the trimer in ELISA, and four of the mAbs potently neutralized the BG505 Env pseudovirus (PV) and SHIV. The four neutralizing mAbs were clonally related and targeted the 465 glycan hole to varying degrees, mimicking the serum. The data demonstrate that the C3/465 glycan hole cluster was the dominant neutralization target in high titer protected RM, despite other co-circulating neutralizing and non-neutralizing specificities. The isolation of a neutralizing mAb family argues that clonotype expansion occurred during BG505 SOSIP immunization, leading to high titer, protective nAb and setting a desirable benchmark for HIV vaccines.     

On the genetics of rosette pattern in guinea pigs

Summary New data on the heredity of rosette pattern in guinea pigs and a critical review of the data ofPictet andFerrero support the conclusions reached in 1916 on the genetics of the major variations of this character.The results ofPictet andFerrero fully confirm the existence of the primary pair of alleles R, r and are so treated by them in their more recent papers. There is strong evidence that the rough inhibiting factor M (of wild species ofCavia and of many guinea pigs) was present in their stock, in certain smooths which transmitted roughness (R-MM) and in the types described as lisses à crête and monorosettes (R-Mm) but was not recognized. This gene was clearly much less common than in my stocks.Their stocks on the other hand seem to have exhibited more variability in the high grades of roughness and to have reached somewhat higher grades than I have observed. They attribute these variations to two new pairs of genes G, g and D, d, the former said to distinguish two patterns on the trunk, the latter, grades of roughness of the head. The data as presented, contain contradictions in both cases. Nevertheless they indicate segregation in their stock of a pair of alleles distinguishing the highest grade of fancier's rough (RRmmGG), from ordinary high grades (RRmmgg). The contradictions may perhaps be due to overlap. No judgment of the validity of genes D, d can be reached without presentation of data showing the breeding results for trunk and head rosettes simultaneously.     

Elicitation of potent serum neutralizing antibody responses in rabbits by immunization with an HIV-1 clade C trimeric Env derived from an Indian elite neutralizer

Evaluating the structure-function relationship of viral envelope (Env) evolution and the development of broadly cross-neutralizing antibodies (bnAbs) in natural infection can inform rational immunogen design. In the present study, we examined the magnitude and specificity of autologous neutralizing antibodies induced in rabbits by a novel HIV-1 clade C Env protein (1PGE-THIVC) vis-à-vis those developed in an elite neutralizer from whom the env sequence was obtained that was used to prepare the soluble Env protein. The novel 1PGE-THIVC Env trimer displayed a native like pre-fusion closed conformation in solution as determined by small angle X-ray scattering (SAXS) and negative stain electron microscopy (EM). This closed spike conformation of 1PGE-THIVC Env trimers was correlated with weak or undetectable binding of non-neutralizing monoclonal antibodies (mAbs) compared to neutralizing mAbs. Furthermore, 1PGE-THIVC SOSIP induced potent neutralizing antibodies in rabbits to autologous virus variants. The autologous neutralizing antibody specificity induced in rabbits by 1PGE-THIVC was mapped to the C3/V4 region (T362/P401) of viral Env. This observation agreed with electron microscopy polyclonal epitope mapping (EMPEM) of the Env trimer complexed with IgG Fab prepared from the immunized rabbit sera. Our study demonstrated neutralization of sequence matched and unmatched autologous viruses by serum antibodies induced in rabbits by 1PGE-THIVC and also highlighted a comparable specificity for the 1PGE-THIVC SOSIP trimer with that seen with polyclonal antibodies elicited in the elite neutralizer by negative-stain electron microscopy polyclonal epitope (ns-EMPEM) mapping.