Multiple-parallel-protease digestion coupled with high-resolution mass spectrometry: An approach towards comprehensive peptide mapping of therapeutic mAbs.

Therapeutic monoclonal antibodies (mAbs) are structurally large and complex molecules. To be safe and efficacious, a biosimilar mAb must show high similarity to its reference product in Critical Quality Attributes (CQA). mAbs are highly sensitive to protein expression, production, manufacturing, supply chain, and storage conditions. All these factors make biosimilar mAbs intrinsically susceptible for variability during production. Accordingly, several lots of references and tests are required to establish the biosimilarity of a test mAb. The primary structure is a CQA of a mAb affecting its safety and efficacy. Here, we apply peptide mapping as an analytical method to decipher the primary structure and associated modifications for a quick quality assessment of TrastuzumAb and RituximAb innovator and biosimilar. A multiple-parallel-protease digestion strategy followed by high-resolution mass spectrometric analysis consistently achieved 100% sequence coverage along with reliable detection of post-translational modifications. Additionally, the use of supporting methods such as intact mass analysis and circular dichroism helped us to decipher the primary and higher order structures of these mAbs. We identify discernible variations in the profile of the innovator and biosimilar mAbs and validate the method for quick yet deep comparability analysis of the primary structure of biosimilar mAbs sold in the market. SIGNIFICANCE: Peptide mapping using bottom-up approach is one of the most common methods for the characterization of therapeutic monoclonal antibodies. Herein, we describe a multi-parallel-protease digestion strategy using a combination of five different proteases followed by high-resolution mass spectrometric analysis with TrastuzumAb and RituximAb as an example. This resulted in a comprehensive identification of peptides with increased reliability and identification of different PTMs. Additional supporting orthogonal methods like intact mass and higher-order structure analysis helped evaluate broader conformational properties.

A complex karyotype with t(11;12)(q23;p13) translocation with coexistent clones of deletion 5q and cryptic deletion 7q in acute myeloid leukemia.

We report a rare case of acute myeloid leukemia (AML) with a cytogenetically complex karyotype with coexistence of KMT2A/MLL Mixed Lineage Leukemia (11q23) rearrangement with 5q deletion and 7q deletion as unrelated clones along with evolution of a subclone with translocation between chromosomes 6 and 17. A novel MLL fusion partner region 12p13 was identified in a 52 year old woman who presented with pyrexia of unknown origin. Unraveling the complexity of genomic alterations occurring in AML patients will lead to better understanding of leukemic transformation and identification of subsets of patients that may respond differently to therapy.

Why Class Formation Occurs in Humans but Not among Other Primates : A Primate Coalitions Model.

Most human societies exhibit a distinct class structure, with an elite, middle classes, and a bottom class, whereas animals form simple dominance hierarchies in which individuals with higher fighting ability do not appear to form coalitions to "oppress" weaker individuals. Here, we extend our model of primate coalitions and find that a division into a bottom class and an upper class is inevitable whenever fitness-enhancing resources, such as food or real estate, are exploitable or tradable and the members of the bottom class cannot easily leave the group. The model predicts that the bottom class has a near flat, low payoff and always comprises at least half the society. The upper class may subdivide into one or more middle class(es), resulting in improved payoff for the topmost members (elite). The model predicts that the bottom class on its own is incapable of mounting effective counter-coalitions against the upper class, except when receiving support from dissatisfied members of the middle class(es). Such counter-coalitions can be prevented by keeping the payoff to the lowest-ranked members of the middle classes (through concessions) well above that of the bottom class. This simple model explains why classes are also absent in nomadic hunter-gatherers and predominate in (though are not limited to) societies that produce and store food. Its results also agree well with various other known features of societies with classes.

Genetic analysis of rotavirus G2P[4] strains in Pune, Western India: circulation of a novel reassortant bearing E6 NSP4 genotype.

In India, G2P[4] strains are known to be the second most predominant group A rotaviruses causing acute gastroenteritis among children. This study was performed to determine the diversity within VP7(G), VP4(P), VP6(I) and NSP4(E) genes of 16 G2P[4] rotavirus strains detected in children hospitalized for acute gastroenteritis in Pune, Western India during 2009-2013. Fourteen strains showed G2-P[4]-I2-E2 and two strains showed G2-P[4]-I2-E6 genotype constellation. Phylogenetic analysis showed their clustering into G2-IV-a3, P[4]-5bi/ii, I2-3ii and E2-4i/ii or E6 genotypes/lineages. These data reveal inter- and/or intra-genotypic variations in a genogroup-2 constellation of G2P[4] rotavirus strains circulating in Pune, Western India, providing evidence of a novel G2P[4] reassortant bearing a rare NSP4 genotype, E6 during 2009-2013.

Full genomic analysis of G1P[8] rotavirus strains recovered from rotavirus vaccinated and non-vaccinated children hospitalized for acute gastroenteritis in Pune, western India.

G1P[8] rotaviruses are predominant in causing diarrheal infections in humans all over the world. This study reports the analysis of complete genomes of G1P[8] strains, two each recovered from Rotarix™ vaccine recipients and non-recipients hospitalized for acute gastroenteritis in Pune, western India. All four strains showed a genogroup-1 backbone with intra-genotypic diversity in the VP7 and VP4 gene segments and a homogeneous constellation of the internal gene segments. A divergence in the range of 1.4-17.3% from Rotarix™ vaccine strain was revealed by structural and non-structural genes of the strains at nucleotide and amino acid level. These data reflect ability of such G1P[8] strains to cause rotavirus infections in humans.

A model for warfare in stratified small-scale societies: The effect of within-group inequality.

In order to predict the features of non-raiding human warfare in small-scale, socially stratified societies, we study a coalitionary model of war that assumes that individuals participate voluntarily because their decisions serve to maximize fitness. Individual males join the coalition if war results in a net economic and thus fitness benefit. Within the model, viable offensive war ensues if the attacking coalition of males can overpower the defending coalition. We assume that the two groups will eventually fuse after a victory, with ranks arranged according to the fighting abilities of all males and that the new group will adopt the winning group's skew in fitness payoffs. We ask whether asymmetries in skew, group size and the amount of resources controlled by a group affect the likelihood of successful war. The model shows, other things being equal, that (i) egalitarian groups are more likely to defeat their more despotic enemies, even when these are stronger, (ii) defection to enemy groups will be rare, unless the attacked group is far more despotic than the attacking one, and (iii) genocidal war is likely under a variety of conditions, in particular when the group under attack is more egalitarian. This simple optimality model accords with several empirically observed correlations in human warfare. Its success underlines the important role of egalitarianism in warfare.

Molecular characterization of emerging G9P[4] rotavirus strains possessing a rare E6 NSP4 or T1 NSP3 genotype on a genogroup-2 backbone using a refined classification framework.

Rotavirus infections associated with unusual strains are an emerging concern in rotavirus vaccination programmes. Recently, an increase in circulation of unusual G9P[4] strains was reported from different regions of India, placing this genotype in third position, after G1P[8] and G2P[4], of the most common rotavirus strains. The aim of the present study was to analyse the complete genomic constellation of three G9P[4] strains (RV09, RV10 and RV11), determine their genetic relatedness to other genogroup-2 strains and understand the evolution of a rare E6 and other NSP4 genotypes. All strains revealed the presence of a genogroup-2 backbone, with RV09 constituting the NSP3 T1 genotype and RV10 and RV11 bearing the NSP4 E6 genotype. A refined criterion adopted to classify the nine internal gene segments of G2P[4] and non-G2P[4] strains with the genogroup-2 backbone into lineages and sub-lineages indicated divergence of >8 % (except NSP1: >5.5 %) for lineages and >3 % for sub-lineages. The VP1 and/or VP3 genes of study strains showed close relationships with animal-like human rotaviruses. The estimated evolutionary rate for the NSP4 E6 genotype was marginally higher (3.78×10-3 substitutions per site per year) than that of genotypes E1 (2.6×10-3 substitutions per site per year) and E2 (3.06×10-3 substitutions per site per year), suggesting a step towards adaptation of E6 on a genogroup-2 backbone. The time and origin of the most recent common ancestor of E6 genotype were estimated to be 1981 and South Asia, respectively. Full-genome and evolutionary analyses performed in this study for G9P[4] strains will help better understand the extent of gene reassortment and origin in unusual rotavirus strains that may remain viable and cause infections in humans.

Rotavirus Infection in Children with Acute Gastroenteritis in Aurangabad, Central Maharashtra.

OBJECTIVE: To determine the prevalence of rotavirus diarrhea and its genotypes in children from Aurangabad, India. METHODS: Stool samples collected during 2012-2013 from 168 children, aged ?3 years, were tested by ELISA to detect rotavirus. Rotavirus strains were genotyped by multiplex reverse-transcription polymerase chain reaction. RESULTS: Stool samples from 20 (11.9%) children tested positive for rotavirus. Rotavirus positivity was higher among the children aged 0-12 months than those in 13-24 and 25-36 months. Severity of disease was moderate in both rotavirus-infected and uninfected children. Genotype G1P[8] combination was detected predominantly in circulation. CONCLUSIONS: Rotavirus diarrhea was caused mainly by G1P[8] strains during 2012-2013 in Aurangabad, Central Maharashtra, India.

The Conditions Favoring Between-Community Raiding in Chimpanzees, Bonobos, and Human Foragers.

Chimpanzees, bonobos, and human foragers share a fission-fusion social system and a mating system of joint male resource defense polygyny. Within-community skew in male strength varies among and within species. In this study, we extend a mathematical model of within-group male coalition formation among primates to derive the conditions for between-community conflicts in the form of raids. We show that the main factor affecting the presence of successful raiding is the likelihood of major discrepancies in party strength, which are set by party size distributions (and thus community size) and the skew in strength. This study confirms the functional similarities between the raiding of chimpanzees and human foragers, and it supports the "imbalance of power" hypothesis for raiding. However, it also proposes two amendments to this model. First, the absence of raiding in bonobos may be attributable more to potential female involvement in defense against raids, which increases the size of defensive coalitions. Second, the model attributes some of the raiding in humans to major contrasts in instantaneous fighting ability created by surprise raids on unarmed victims; it also draws attention to the distinction between minor raids and major raids that involve multiple bands of the same community.

Why do chimpanzee males attack the females of neighboring communities?

Our closest nonhuman primate relatives, chimpanzees, engage in potentially lethal between-group conflict; this collective aggressive behavior shows parallels with human warfare. In some communities, chimpanzee males also severely attack and even kill females of the neighboring groups. This is surprising given their system of resource defense polygyny, where males are expected to acquire potential mates. We develop a simple mathematical model based on reproductive skew among primate males to solve this puzzle. The model predicts that it is advantageous for high-ranking males but not for low-ranking males to attack females. It also predicts that more males gain a benefit from attacking females as the community's reproductive skew decreases, i.e., as mating success is more evenly distributed. Thus, fatal attacks on females should be concentrated in communities with low reproductive skew. These attacks should also concur with between-community infanticide. A review of the chimpanzee literature provides enough preliminary support for this prediction to warrant more detailed testing.

Changing trends in circulating rotavirus strains in Pune, western India in 2009-2012: emergence of a rare G9P[4] rotavirus strain.

BACKGROUND: A vast diversity in rotaviruses at inter- and intra-genotypic level underscores the need for monitoring of circulating rotavirus strains. The aim of this study was to update the data on rotavirus disease and strains for the period from January 2009 to December 2012 in Pune, western India which has been one of the sites of the Indian Rotavirus Strain Surveillance Network since November 2005. METHODS: Children aged <5 years admitted for acute gastroenteritis in three different hospitals from Pune city were included in the study. The stool specimens were collected and tested for rotavirus antigen by a commercial enzyme immunoassay. The rotavirus strains were genotyped by multiplex reverse transcription polymerase chain reaction. RESULTS: During the study period, we found 35.1% of 685 stool specimens contained rotavirus antigen. Frequency of rotavirus detection was greatest (58.5%) among children aged 7-12 months. The G1P[8] (31.4%), G2P[4] (20.2%) and G9P[8] (11.8%) strains were the most common types. We noted predominance of G1P[8] strains (39.6%-46.1%) in all the years of study except 2009 wherein G9P[8] strains scored highest level (15.3%). Subsequent to this, we identified G9P[8] strains at the second highest position in 2010, their sudden decline and rise in G9P[4] strains in 2011-2012. We detected G12 strains in combination with P[6] and P[8] at variable rates (0-10.2%) and highest level (27.1%) of mixed rotavirus infections in 2009 as compared to 2010-2012 (0-3.8%). CONCLUSION: The study highlights the huge burden of rotavirus disease and changing profile of circulating rotavirus strains displaying emergence of G9P[4] reassortant strains in Pune, western India and emphasizes the need to analyze the entire genomic constellation of rotavirus strains for better evaluation of the impact of rotavirus.

Social organization and the evolution of cumulative technology in apes and hominins.

Culturally supported accumulation (or ratcheting) of technological complexity is widely seen as characterizing hominin technology relative to that of the extant great apes, and thus as representing a threshold in cultural evolution. To explain this divide, we modeled the process of cultural accumulation of technology, which we defined as adding new actions to existing ones to create new functional combinations, based on a model for great ape tool use. The model shows that intraspecific and interspecific variation in the presence of simple and cumulative technology among extant orangutans and chimpanzees is largely due to variation in sociability, and hence opportunities for social learning. The model also suggests that the adoption of extensive allomaternal care (cooperative breeding) in early Pleistocene Homo, which led to an increase in sociability and to teaching, and hence increased efficiency of social learning, was enough to facilitate technological ratcheting. Hence, socioecological changes, rather than advances in cognitive abilities, can account for the cumulative cultural changes seen until the origin of the Acheulean. The consequent increase in the reliance on technology could have served as the pacemaker for increased cognitive abilities. Our results also suggest that a more important watershed in cultural evolution was the rise of donated culture (technology or concepts), in which technology or concepts was transferred to naïve individuals, allowing them to skip many learning steps, and specialization arose, which allowed individuals to learn only a subset of the population's skills.

A model for the evolution of developmental arrest in male orangutans.

Male Sumatran orangutans (Pongo abelii) may delay for many years the acquisition of the full array of secondary sexual traits, including their characteristic cheek flanges. Such flexible developmental arrest is unique among male primates. Among male Bornean orangutans (Pongo pygmaeus) such long delays appear less common. Here, we develop a simple model to identify the conditions under which developmental arrest can be adaptive. We show that the baseline strategy (i.e., males are not susceptible to arrest) cannot be invaded by the flexible strategy (i.e., males can arrest their development when the conditions are unfavorable) when the potential for high-ranking unflanged or flanged males to monopolize sexual access to females is low. In contrast, at high monopolization potential, the flexible strategy is the evolutionarily stable strategy. We also derive the proportion of flanged males in the population for each combination of monopolization values. This model concurs with field data that found a different monopolization potential between Bornean and Sumatran flanged males and a lower proportion of flanged males in the population in Sumatran orangutans. Pronounced developmental arrest is linked to very low adult mortality, which explains why it is so limited in its taxonomic distribution.

Mating strategies in primates: a game theoretical approach to infanticide.

Infanticide by newly immigrated or newly dominant males is reported among a variety of taxa, such as birds, rodents, carnivores and primates. Here we present a game theoretical model to explain the presence and prevalence of infanticide in primate groups. We have formulated a three-player game involving two males and one female and show that the strategies of infanticide on the males' part and polyandrous mating on the females' part emerge as Nash equilibria that are stable under certain conditions. Moreover, we have identified all the Nash equilibria of the game and arranged them in a novel hierarchical scheme. Only in the subspace spanned by the males are the Nash equilibria found to be strict, and hence evolutionarily stable. We have therefore proposed a selection mechanism informed by adaptive dynamics to permit the females to transition to, and remain in, optimal equilibria after successive generations. Our model concludes that polyandrous mating by females is an optimal strategy for the females that minimizes infanticide and that infanticide confers advantage to the males only in certain regions of parameter space. We have shown that infanticide occurs during turbulent changes accompanying male immigration into the group. For changes in the dominance hierarchy within the group, we have shown that infanticide occurs only in primate groups where the chance for the killer to sire the next infant is high. These conclusions are confirmed by observations in the wild. This model thus has enabled us to pinpoint the fundamental processes behind the reproductive decisions of the players involved, which was not possible using earlier theoretical studies.

Rhesus monkeys (Macaca mulatta) lack expertise in face processing.

Faces are salient stimuli for primates that rely predominantly on visual cues for recognizing conspecifics and maintaining social relationships. While previous studies have shown similar face discrimination processes in chimpanzees and humans, data from monkeys are unclear. Therefore, three studies examined face processing in rhesus monkeys using the face inversion effect, a fractured face task, and an individual recognition task. Unlike chimpanzees and humans, the monkeys showed a general face inversion effect reflected by significantly better performance on upright compared to inverted faces (conspecifics, human and chimpanzees faces) regardless of the subjects' expertise with those categories. Fracturing faces alters first- and second-order configural manipulations whereas previous studies in chimpanzees showed selective deficits for second-order configural manipulations. Finally, when required to individuate conspecific's faces, i.e., matching two different photographs of the same conspecific, monkeys showed poor discrimination and repeated training. These results support evolutionary differences between rhesus monkeys and Hominoids in the importance of configural cues and their ability to individuate conspecifics' faces, suggesting a lack of face expertise in rhesus monkeys.

A model for tool-use traditions in primates: implications for the coevolution of culture and cognition.

Inspired by the demonstration that tool-use variants among wild chimpanzees and orangutans qualify as traditions (or cultures), we developed a formal model to predict the incidence of these acquired specializations among wild primates and to examine the evolution of their underlying abilities. We assumed that the acquisition of the skill by an individual in a social unit is crucially controlled by three main factors, namely probability of innovation, probability of socially biased learning, and the prevailing social conditions (sociability, or number of potential experts at close proximity). The model reconfirms the restriction of customary tool use in wild primates to the most intelligent radiation, great apes; the greater incidence of tool use in more sociable populations of orangutans and chimpanzees; and tendencies toward tool manufacture among the most sociable monkeys. However, it also indicates that sociable gregariousness is far more likely to produce the maintenance of invented skills in a population than solitary life, where the mother is the only accessible expert. We therefore used the model to explore the evolution of the three key parameters. The most likely evolutionary scenario is that where complex skills contribute to fitness, sociability and/or the capacity for socially biased learning increase, whereas innovative abilities (i.e., intelligence) follow indirectly. We suggest that the evolution of high intelligence will often be a byproduct of selection on abilities for socially biased learning that are needed to acquire important skills, and hence that high intelligence should be most common in sociable rather than solitary organisms. Evidence for increased sociability during hominin evolution is consistent with this new hypothesis.

Shape anisotropy of lipid molecules and voids.

Biological polymers, viz., proteins, membranes and micelles exhibit structural discontinuities in terms of spaces unfilled by the polymeric phase, termed voids. These voids exhibit dynamics and lead to interesting properties which are experimentally demonstrable. In the specific case of phospholipid membranes, numerical simulations on a two-dimensional model system showed that voids are induced primarily due to the shape anisotropy in binary mixtures of interacting disks. The results offer a minimal description required to explain the unusually large permeation seen in liposomes made up of specific lipid mixtures (Mathai & Sitaramam, 1994). The results are of wider interest, voids being ubiquitous in biopolymers.

An epidemiological study of pulmonary function tests in geriatric population of central India.

We have studied Pulmonary Function Tests (PFTs) namely Vital Capacity (VC). Forced Vital Capacity (FVC), and Forced Expiratory Volume in First Second (FEV1). Forced Expiratory Flow(FEF 25-50%) in 1200 elderly subjects above 60 years of age of which 570 were females and 630 males. Mean age was 69.22 +/- 5.57 years in males and 68.77 +/- 5.44 in females. The mean value of ventilatory parameters were as follows-1) VC 2.99 +/- 0.5 lt in males and 1.89 +/- 0.29 lt in females. 2) FVC 2.69 +/- 0.58 lt. in males and 1.76 +/- 0.21 lt in females. 3) FEV1/FVC% 83.82 +/- 10.62% in males and 83.37 +/- 11.93% in females. 4) FEF 25-75% was 2.81 +/- 1.20 lt/sec in males and 2.13 +/- 1.27 lt/sec. Physical as well as ventilatory parameters were less in females than for males. The correlation of age with VC and FEV1 was highly significant (P < 0.01) but with FVC was not significant (P > 0.05). The correlation of height, weight and body surface area was not significant with any ventilatory parameter (P > 0.05). Multiple regression equations for VC, FVC and FEV1 were formulated for males and females taking height and age as variables. The predicted values correlated excellently with observed values.

Mode locking of spatiotemporally periodic orbits in coupled sine circle map lattices.

We study the organization of mode-locked intervals corresponding to the stable spatiotemporally periodic solutions in a lattice of diffusively coupled sine circle maps with periodic boundary conditions. Spatially periodic initial conditions settle down to spatiotemporally periodic solutions over large regions of the parameter space. In the case of synchronized solutions resulting from synchronized initial conditions, the mode-locked intervals have been seen to follow strict Farey ordering in the temporal periods. However, the nature of the organization of the mode-locked intervals corresponding to higher spatiotemporal periods is highly dependent on initial conditions and on system parameters. Farey ordering in the temporal periods is seen at low coupling for mode-locked intervals of all spatial periods. On the other hand, stable spatial period two solutions show an interesting reversal of Farey ordering at high values of coupling. Other spatially periodic solutions show a complete departure from Farey ordering at high coupling. We also examine the issue of completeness of the mode-locked intervals via a calculation of the fractal dimension of the complement of the mode-locked intervals as a function of the coupling epsilon and the nonlinearity parameter K. Our results are consistent with completeness over a range of values for these parameters. Spatiotemporally periodic solutions of the traveling wave type have their own organization in the parameter space. Novel bifurcations to other types of solutions are seen in the mode-locked intervals. We discuss various features of these bifurcations. We also define a set of new variables using which an analytic treatment of the bifurcations along the Omega=0 line is carried out.