Length-independent structural similarities enrich the antibody CDR canonical class model

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach.

To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ～20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.     

Milking strategy in subantarctic fur seals Arctocephalus tropicalis breeding on Amsterdam Island: evidence from changes in milk composition.

Milk composition was investigated throughout the 10-mo pup-rearing period in subantarctic fur seals (Arctocephalus tropicalis) breeding on Amsterdam Island. The mean milk composition was 42.8% +/- 5.7% lipid, 12.1% +/- 1.5% protein, and 42.6% +/- 7.3% water. Subantarctic fur seals breeding on Amsterdam Island produced one of the richest milks ever reported in otariids (20.4 +/- 2.9 kJ/g), with lipid content contributing 85% of total gross energy. The high lipid levels measured in the milk of subantarctic fur seals breeding on Amsterdam Island is consistent (i) with the relatively long time lactating females spend at sea, due to the relatively poor local trophic conditions near the colony that necessitate that they travel long distances to reach the foraging grounds, and (ii) with the consequently short time mothers spend with their pups ashore. Milk composition changed according to the time mothers were fasting ashore: milk produced during the first 2 d spent ashore, when more than 80% of milk transfer occurred, had higher levels of lipids, proteins, and gross energy than milk produced later during the visit ashore, suggesting that the pups were fed with two types of milk during a suckling period. Throughout the year, mothers in good condition produced milk of higher lipid content than others, suggesting that individual foraging skills contribute to enhance milk quality. Milk lipid and gross energy content varied with pup age, according to quadratic relationships, increasing during the earlier stages of lactation before reaching asymptotic values when pups were 180 d old. The stage of lactation appears to be a better predictor of milk lipid content than the duration of the preceding foraging trip, suggesting that either changes in the nutritional requirements of the pup and/or seasonal changes in trophic conditions act on milk composition. These changes in milk quality may also be related to changes in maternal care; lactating subantarctic fur seals apparently reallocate their body reserves toward gestation rather than lactation at the end of the pup-rearing period.     

Phenotypic plasticity of body size in Drosophila: effects of a daily periodicity of growth temperature in two sibling species

Abstract. Variation of wing and thorax length under thermoperiodic growth conditions was analysed in four strains of two sibling species, Drosophila melanogaster and D. simulans , from two European localities. Results were compared to those obtained with constant temperatures ranging from 12 to 31 °C.
Under constant temperatures the data basically confirmed previous results: concave reaction norms for wing and thorax length; a monotonically decreasing norm for wing : thorax ratio; and an increasing norm for sex dimorphism (female : male ratio). Phenotypic variability was maximum at extreme temperatures and minimum at middle ones. Slight differences were observed according to the geographical origin: the difference between strains from Bordeaux (France) and Cordoba (Spain) was maximum at low temperatures but disappeared at about 28 °C.
According to the temperatures chosen, alternating thermal regimens had either no effect or produced a significant size reduction, probably reflecting a periodic stress. The magnitude of this effect was proportional to the amplitude of the thermoperiod but not to the quality (cold or heat) of the stress. In a similar way, the wing : thorax ratio was either not modified or reduced significantly, indicating that wing length was relatively more affected than thorax length by alternating thermal regimens. Sex dimorphism also showed either no change or a significant increase, indicating that males were relatively more reactive than females to alternating conditions. Finally, regimens of broad amplitudes increased the phenotypic variability, again an indication of stressful effects. All these observations should be taken into account when analysing phenotypic variability in nature and trying to understand natural selection in wild-living populations.     

The mechanical properties of cranial bone: The effect of loading rate and cranial sampling position

Linear and depressed skull fractures are frequent mechanisms of head injury and are often associated with traumatic brain injury. Accurate knowledge of the fracture of cranial bone can provide insight into the prevention of skull fracture injuries and help aid the design of energy absorbing head protection systems and safety helmets. Cranial bone is a complex material comprising of a three-layered structure: external layers consist of compact, high-density cortical bone and the central layer consists of a low-density, irregularly porous bone structure.In this study, cranial bone specimens were extracted from 8 fresh-frozen cadavers (F=4, M=4; 81±11 years old). 63 specimens were obtained from the parietal and frontal cranial bones. Prior to testing, all specimens were scanned using a μCT scanner at a resolution of 56.9 μm. The specimens were tested in a three-point bend set-up at different dynamic speeds (0.5, 1 and 2.5 m/s). The associated mechanical properties that were calculated for each specimen include the 2nd moment of inertia, the sectional elastic modulus, the maximum force at failure, the energy absorbed until failure and the maximum bending stress. Additionally, the morphological parameters of each specimen and their correlation with the resulting mechanical parameters were examined.It was found that testing speed, strain rate, cranial sampling position and intercranial variation all have a significant effect on some or all of the computed mechanical parameters. A modest correlation was also found between percent bone volume and both the elastic modulus and the maximum bending stress.     

On extremum seeking in bioprocesses with multivalued cost functions

Finding optimal operating modes for bioprocesses has been, for a long time, a relevant issue in bioengineering. The problem is of special interest when it implies the simultaneous optimization of competing objectives. In this paper, we address the problem of finding optimal steady states that achieve the best tradeoff between yield and productivity by using nonmodel ‐ based extremum‐seeking control with semiglobal practical stability and convergence properties. A special attention is paid to processes with multiple steady states and multivalued cost functions. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Discoidin domain receptor 1 controls linear invadosome formation via a Cdc42–Tuba pathway

Accumulation of type I collagen fibrils in tumors is associated with an increased risk of metastasis. Invadosomes are F-actin structures able to degrade the extracellular matrix. We previously found that collagen I fibrils induced the formation of peculiar linear invadosomes in an unexpected integrin-independent manner. Here, we show that Discoidin Domain Receptor 1 (DDR1), a collagen receptor overexpressed in cancer, colocalizes with linear invadosomes in tumor cells and is required for their formation and matrix degradation ability. Unexpectedly, DDR1 kinase activity is not required for invadosome formation or activity, nor is Src tyrosine kinase. We show that the RhoGTPase Cdc42 is activated on collagen in a DDR1-dependent manner. Cdc42 and its specific guanine nucleotide-exchange factor (GEF), Tuba, localize to linear invadosomes, and both are required for linear invadosome formation. Finally, DDR1 depletion blocked cell invasion in a collagen gel. Altogether, our data uncover an important role for DDR1, acting through Tuba and Cdc42, in proteolysis-based cell invasion in a collagen-rich environment.     

First Evidence of a Volatile Sex Pheromone in Lady Beetles

To date, volatile sex pheromones have not been identified in the Coccinellidae family; yet, various studies have suggested that such semiochemicals exist. Here, we collected volatile chemicals released by virgin females of the multicolored Asian lady beetle, Harmonia axyridis (Pallas), which were either allowed or not allowed to feed on aphids. Virgin females in the presence of aphids, exhibited “calling behavior”, which is commonly associated with the emission of a sex pheromone in several Coleoptera species. These calling females were found to release a blend of volatile compounds that is involved in the remote attraction (i.e., from a distance) of males. Gas Chromatography-Mass Spectrometry (GC-MS) analyses revealed that (–)-β-caryophyllene was the major constituent of the volatile blend (ranging from 80 to 86%), with four other chemical components also being present; β-elemene, methyl-eugenol, α-humulene, and α-bulnesene. In a second set of experiments, the emission of the five constituents identified from the blend was quantified daily over a 9-day period after exposure to aphids. We found that the quantity of all five chemicals significantly increased across the experimental period. Finally, we evaluated the activity of a synthetic blend of these chemicals by performing bioassays which demonstrated the same attractive effect in males only. The results confirm that female H. axyridis produce a volatile sex pheromone. These findings have potential in the development of more specific and efficient biological pest-control management methods aimed at manipulating the behavior of this invasive lady beetle.     

Detection and structural characterization of insulin prefibrilar oligomers using surface enhanced Raman spectroscopy

In vitro fibril formation typically exhibits a lag phase followed by a rapid elongation phase. Soluble prefibrilar oligomers form as multiple assembly states occur during the lag phase and, after forming a nucleus, rapidly propagate into amyloid aggregates and fibrils. The structure and morphology of amyloid fibrils have been extensively characterized over the last decades, while little is known about the structural organization of the prefibrilar oligomers or their multiple assembly states. The main difficulty in structural characterization of prefibrilar aggregates is their low concentration (pmolar) and their continual reactive conversion. Herein we overcome these difficulties by utilizing Surface‐Enhanced Raman Spectroscopy (SERS) with a model amyloid peptide, insulin. SERS is a powerful analytic tool that is able to provide detection of small molecules down to a single‐molecule level. Using SERS we found that during the 3 lag phase before the onset of insulin fibril formation, the amount of insulin oligomers increased more than twice after the first hour of incubation under fibrillation conditions (pH 1.6, 65°C) and then slowly decreased with time. The latter finding is kinetically linked to the conversion of the prefibrilar oligomers into fibril species. This study provides valuable new information about the time‐dependent structural organization of insulin oligomers and demonstrates the power and potential of SERS for detection and structural characterization of biological specimens present at low concentrations. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:488–495, 2014     

How Does Pollen Chemistry Impact Development and Feeding Behaviour of Polylectic Bees?

Larvae and imagos of bees rely exclusively on floral rewards as a food source but host-plant range can vary greatly among bee species. While oligolectic species forage on pollen from a single family of host plants, polylectic bees, such as bumblebees, collect pollen from many families of plants. These polylectic species contend with interspecific variability in essential nutrients of their host-plants but we have only a limited understanding of the way in which chemicals and chemical combinations influence bee development and feeding behaviour. In this paper, we investigated five different pollen diets (Calluna vulgaris, Cistus sp., Cytisus scoparius, Salix caprea and Sorbus aucuparia) to determine how their chemical content affected bumblebee colony development and pollen/syrup collection. Three compounds were used to characterise pollen content: polypeptides, amino acids and sterols. Several parameters were used to determine the impact of diet on micro-colonies: (i) Number and weight of larvae (total and mean weight of larvae), (ii) weight of pollen collected, (iii) pollen efficacy (total weight of larvae divided by weight of the pollen collected) and (iv) syrup collection. Our results show that pollen collection is similar regardless of chemical variation in pollen diet while syrup collection is variable. Micro-colonies fed on S. aucuparia and C. scoparius pollen produced larger larvae (i.e. better mates and winter survivors) and fed less on nectar compared to the other diets. Pollen from both of these species contains 24-methylenecholesterol and high concentrations of polypeptides/total amino acids. This pollen nutritional “theme” seems therefore to promote worker reproduction in B. terrestris micro-colonies and could be linked to high fitness for queenright colonies. As workers are able to selectively forage on pollen of high chemical quality, plants may be evolutionarily selected for their pollen content, which might attract and increase the degree of fidelity of generalist pollinators, such as bumblebees.