Simultaneous identification of growth law and estimation of its rate parameter for biological growth data: a new approach

Scientific formalizations of the notion of growth and measurement of the rate of growth in living organisms are age-old problems. The most frequently used metric, “Average Relative Growth Rate” is invariant under the choice of the underlying growth model. Theoretically, the estimated rate parameter and relative growth rate remain constant for all mutually exclusive and exhaustive time intervals if the underlying law is exponential but not for other common growth laws (e.g., logistic, Gompertz, power, general logistic). We propose a new growth metric specific to a particular growth law and show that it is capable of identifying the underlying growth model. The metric remains constant over different time intervals if the underlying law is true, while the extent of its variation reflects the departure of the assumed model from the true one. We propose a new estimator of the relative growth rate, which is more sensitive to the true underlying model than the existing one. The advantage of using this is that it can detect crucial intervals where the growth process is erratic and unusual. It may help experimental scientists to study more closely the effect of the parameters responsible for the growth of the organism/population under study.     

PAHs,OCPs and PCBs in sediments from three catchments in Durban,South Africa

Polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) were analysed from sediment samples collected in 2012 from rivers, surface runoff canals and estuaries in three highly urbanised catchments in durban, KwaZulu-Natal, South Africa. PAHs were ubiquitous, at concentrations between 36–6 800 ng g^?1 dry mass (dm). Congener ratio diagnosis suggests the PAHs were derived predominantly from pyrogenic sources. Four OCPs and/or their metabolites were detected at varying frequencies and concentrations. Of these, dichlorodiphenyltrichloroethane (ddT) and metabolites were most frequently detected and were at a high concentration in sediment in some systems. Toxaphene was detected at a high concentration at some sites. The total PCB concentration varied widely, from below the method detection limit to 110 ng g^?1 (dm). Based on the comparison of chemical concentrations to international sediment quality guidelines, PAH, OCP and PCB concentrations in most sediment samples posed a low risk to sediment-dwelling organisms. However, in some instances the risk was moderate or high. It is recommended that these compounds be monitored more frequently and comprehensively in aquatic ecosystems to better understand the ecological and human health implications.     

Characterization ofStreptomyces sp. Strain DRS-1 and its ampicillin transformation product

Incubation of ampicillin with whole cells ofStreptomyces sp. DRS-1 resulted in accumulation of four compounds different from ampicillin. One of them was isolated, purified and partially characterized. On the basis of spectroscopic characteristics,R _F value and antibacterial activity the compound was identified as cephalexin. It could also be obtained from ampicillin by using crude protein extract of the strain.     

Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC

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Control of Pierce's Disease by Phage

Pierce’s Disease (PD) of grapevines, caused by Xylella fastidiosa subsp. fastidiosa (Xf), is a limiting factor in the cultivation of grapevines in the US. There are presently no effective control methods to prevent or treat PD. The therapeutic and prophylactic efficacy of a phage cocktail composed of four virulent (lytic) phages was evaluated for control of PD. Xf levels in grapevines were significantly reduced in therapeutically or prophylactically treated grapevines. PD symptoms ceased to progress one week post-therapeutic treatment and symptoms were not observed in prophylactically treated grapevines. Cocktail phage levels increased in grapevines in the presence of the host. No in planta phage-resistant Xf isolates were obtained. Moreover, Xf mutants selected for phage resistance in vitro did not cause PD symptoms. Our results indicate that phages have great potential for biocontrol of PD and other economically important diseases caused by Xylella.     

Urothelial transdifferentiation to prostate epithelia is mediated by paracrine TGF-β signaling

The embryonic urogenital sinus mesenchyme (UGM) induces prostate epithelial morphogenesis in development. The molecular signals that drive UGM-mediated prostatic induction have not been defined. We hypothesized that the TGF-β signaling directed the prostatic induction. UGM from TGF-β type II receptor stromal conditional knockout mice (Tgfbr2^fspKO) or control mice (Tgfbr2^{floxE2/floxE2}) was recombined with wild-type adult mice bladder urothelial cells. The resulting urothelium associated with Tgfbr2^{floxE2/floxE2} UGM was instructively differentiated into prostatic epithelium, as expected. In contrast, the urothelium associated with Tgfbr2^fspKO UGM permissively maintained the phenotype of bladder epithelial cells. Microarray analysis of UGM tissues suggested the down-regulation of multiple Wnt ligands and the up-regulation of the Wnt antagonist, Wif 1, by the Tgfbr2^fspKO UGM compared with Tgfbr2^{floxE2/floxE2} UGM. The overexpression of Wif-1 by wild-type UGM resulted in the inhibition of prostatic induction. These data suggest that the stromal TGF-β activity mediated by paracrine Wnt is necessary for the induction of prostatic differentiation. As Wnt ligands mediate differentiation and maintain the stem cell phenotype, the contribution of mouse stem cells and somatic cells to prostatic epithelium in the tissue recombination models was tested. The directed differentiation of mouse embryonic stem cells by UGM is suggested by a threshold number of mouse stem cells required in prostatic differentiation. To determine the contribution of somatic cells, the adult bladder epithelial compartment was labeled with green-fluorescent vital dye (CMFDA) and the stem-like cells marked by bromodeoxyuridine (BrdU) label-retention. The resulting prostatic epithelia of the tissue recombinants maintained the CMFDA dye, suggesting minimal cell division. Thus, the UGM can induce endoderm-derived epithelia and stem cells to form prostate through a transdifferentiation mechanism that requires stromal TGF-β signaling to mediate epithelial Wnt activity.     

Ecological factors affect the level and scaling of avian BMR

The basal rate of metabolism (BMR) in 533 species of birds, when examined with ANCOVA, principally correlates with body mass, most of the residual variation correlating with food habits, climate, habitat, a volant or flightless condition, use or not of torpor, and a highland or lowland distribution. Avian BMR also correlates with migratory habits, if climate and a montane distribution is excluded from the analysis, and with an occurrence on small islands if a flightless condition and migration are excluded. Residual variation correlates with membership in avian orders and families principally because these groups are behaviorally and ecologically distinctive. However, the distinction between passerines and other birds remains a significant correlate of avian BMR, even after six ecological factors are included, with other birds having BMRs that averaged 74% of the passerine mean. This combination of factors accounts for 97.7% of the variation in avian BMR. Yet, migratory species that belong to Anseriformes, Charadriiformes, Pelecaniformes, and Procellariiformes and breed in temperate or polar environments have mass-independent basal rates equal to those found in passerines. In contrast, penguins belong to an order of polar, aquatic birds that have basal rates lower than passerines because their flightless condition depresses basal rate. Passerines dominate temperate, terrestrial environments and the four orders of aquatic birds dominate temperate and polar aquatic environments because their high BMRs facilitate reproduction and migration. The low BMRs of tropical passerines may reflect a sedentary lifestyle as much as a life in a tropical climate. Birds have BMRs that are 30-40% greater than mammals because of the commitment of birds to an expensive and expansive form of flight.     

Paradoxical Effect of Pertussis Toxin on the Delayed Hypersensitivity Response to Autoantigens in Mice

Background

Pertussis toxin (PTX), an exotoxin of Bordetella pertussis, enhances the development of experimental autoimmune diseases such as experimental autoimmune uveitis (EAU) and experimental autoimmune encephalomyelitis (EAE) in rodent models. The mechanisms of the promotion of experimental autoimmune diseases by PTX may be based upon PTX-induced disruption of the blood eye/brain barriers facilitating the infiltration of inflammatory cells, the modulation of inflammatory cell migration and the enhancement of the activation of inflammatory cells. We hypothesized that the facilitation of experimental autoimmunity by PTX suggests that its influence on the in vivo immune response to auto-antigen may differ from its influence on non-self antigens.

Methodology/Principal Findings

We have evaluated the effect of PTX on the simultaneous generation of delayed type hypersensitivity (DTH) responses and autoimmune responses to uveitogenic interphotoreceptor retinoid binding protein peptide (IRBP_161–180), encephalitogenic myelin oligodendrocyte glycoprotein peptide (MOG_35–55) or ovalbumin (OVA). PTX injection of mice immunized to IRBP peptide_161–180 led to (i) the development of EAU as shown by histopathology of the retina, (ii) pro-inflammatory cytokine production by splenocytes in response to IRBP peptide _161–180, and (iii) symptomatic EAE in mice immunized with encephalitogenic MOG peptide_35–55. However, mice that received PTX had a reduced DTH response to IRBP_161–180 peptide or MOG peptide_35–55 when challenged distal to the site affected by autoreactive T cells. Moreover, footpad challenge with MOG_35–55 peptide reduced EAE in mice immunized with MOG peptide. In contrast, the use of PTX when immunizing with OVA protein or an OVA immunogenic peptide did not affect the DTH response to OVA.

Conclusions/Significance

The results suggest that that the reduced DTH response in mice receiving PTX may be specific for autoantigens and autoantigen-reactive T cells are diverted away from ectopic sites that received the autoantigen and towards the tissue site of the autoantigen.     

Desiccation tolerance in bovine sperm: A study of the effect of intracellular sugars and the supplemental roles of an antioxidant and a chelator

Desiccation preservation holds promise as a simplified alternative to cryopreservation for the long term storage of cells. We report a study on the protective effects of intracellular and extracellular sugars during bovine sperm desiccation and the supplemental effects of the addition of an antioxidant (catalase) or a chelator (desferal). The goal of the study was to preserve mammalian sperm in a partially or completely desiccated state. Sperm loaded intracellularly with two different types of sugars, trehalose or sucrose, were dried with and without catalase and desferal and evaluated for motility and membrane integrity immediately after rehydration. Intracellular sugars were loaded using ATP induced poration. Drying was performed in desiccator boxes maintained at 11% relative humidity (RH). Results indicated that sperm exhibited improved desiccation tolerance if they were loaded with either intracellular trehalose or sucrose. Survival was further enhanced by the addition of 1 mM desferal to the desiccation buffer. Though sperm motility after drying to low dry basis water fractions (DBWF) did not show significant improvement under any of the tested conditions, there was an increase in the sperm membrane integrity that could be retained after partial desiccation through the use of intracellular sugars and desferal.     

A phylogenetic analysis of Momordica (Cucurbitaceae) in India based on karyo-morphology,nuclear DNA content and rDNA ITS1–5.8S–ITS2 sequences

The infrageneric delimitation of Momordica, a medicinally important genus of Cucurbitaceae, is ill-defined until date. Momordica chromosomes are extremely small and are difficult to stain and visualize because of the dense cytoplasmic background. We have conducted karyomorphometric analysis by EMA method in five Indian Momordica species, and the nuclear genome sizes were estimated by flow cytometry for the first time. The somatic chromosome numbers ranged from 2n = 18 to 56 in the species. We have resolved previously disputed chromosome numbers in M. cymbalaria and M. dioica as 2n = 18 (lowest) and 2n = 56, respectively. Chromosome counts in the other species were re-confirmed as 2n = 22 in M. charantia, 2n = 28 in M. cochinchinensis and 2n = 56 in M. subangulata. The largest genome size was recorded in M. cymbalaria (3.74 pg 2C⁻¹), while the smallest size (0.72 pg 2C⁻¹) was detected in M. charantia var. charantia. The nuclear genome sizes were analysed in comparison to chromosome numbers and total chromosome lengths of the species. Karyomorphometric indices showed comparable symmetric karyotypes in the species except in M. cymbalaria having tendency towards asymmetry. The UPGMA phenogram and principle component analysis based on nuclear DNA contents and karyomorphometric parameters demonstrated interspecies differences, intraspecific distinction within M. charantia varieties and highlighted distinction of M. cymbalaria. This study was further supported by the rDNA ITS sequence-based phylogenetic analysis which revealed the monophyletic origin of the Indian members of Momordica and clarified the intraspecies relationship among the studied members. As a whole, the study brought out new insights on species diversification within the genus Momordica in India and would benefit further studies on biosystematics and plant breeding programmes.