Differential sulfations and epimerization define heparan sulfate specificity in nervous system development

Heparan sulfate proteoglycans (HSPG) are components of the extracellular matrix through which axons navigate to reach their targets. The heparan sulfate (HS) side chains of HSPGs show complex and differentially regulated patterns of secondary modifications, including sulfations of distinct hydroxyl groups and epimerization of an asymmetric carbon atom. These modifications endow the HSPG-containing extracellular matrix with the potential to code for an enormous molecular diversity. Attempting to decode this diversity, we analyzed C. elegans animals lacking three HS-modifying enzymes, glucuronyl C5-epimerase, heparan 6O-sulfotransferase, and 2O-sulfotransferase. Each of the mutant animals exhibit distinct as well as overlapping axonal and cellular guidance defects in specific neuron classes. We have linked individual HS modifications to two specific guidance systems, the sax-3/Robo and kal-1/Anosmin-1 systems, whose activity is dependent on different HS modifications in different cellular contexts. Our results demonstrate that the molecular diversity in HS encodes information that is crucial for different aspects of neuronal development.     

Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase,an Initial Component of the N-End Rule Pathway

The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases.     

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.     

Protein Paucimannosylation Is an Enriched N‐Glycosylation Signature of Human Cancers

While aberrant protein glycosylation is a recognized characteristic of human cancers, advances in glycoanalytics continue to discover new associations between glycoproteins and tumorigenesis. This glycomics‐centric study investigates a possible link between protein paucimannosylation, an under‐studied class of human N‐glycosylation [Man_1‐3GlcNAc₂Fuc_0‐1], and cancer. The paucimannosidic glycans (PMGs) of 34 cancer cell lines and 133 tissue samples spanning 11 cancer types and matching non‐cancerous specimens are profiled from 467 published and unpublished PGC‐LC‐MS/MS N‐glycome datasets collected over a decade. PMGs, particularly Man_2‐3GlcNAc₂Fuc₁, are prominent features of 29 cancer cell lines, but the PMG level varies dramatically across and within the cancer types (1.0–50.2%). Analyses of paired (tumor/non‐tumor) and stage‐stratified tissues demonstrate that PMGs are significantly enriched in tumor tissues from several cancer types including liver cancer (p = 0.0033) and colorectal cancer (p = 0.0017) and is elevated as a result of prostate cancer and chronic lymphocytic leukaemia progression (p < 0.05). Surface expression of paucimannosidic epitopes is demonstrated on human glioblastoma cells using immunofluorescence while biosynthetic involvement of N‐acetyl‐β‐hexosaminidase is indicated by quantitative proteomics. This intriguing association between protein paucimannosylation and human cancers warrants further exploration to detail the biosynthesis, cellular location(s), protein carriers, and functions of paucimannosylation in tumorigenesis and metastasis.     

European springtime temperature synchronises ibex horn growth across the eastern Swiss Alps

Direct effects of climate change on animal physiology, and indirect impacts from disruption of seasonal synchrony and breakdown of trophic interactions are particularly severe in Arctic and Alpine ecosystems. Unravelling biotic from abiotic drivers, however, remains challenging because high‐resolution animal population data are often limited in space and time. Here, we show that variation in annual horn growth (an indirect proxy for individual performance) of 8043 male Alpine ibex (Capra ibex) over the past four decades is well synchronised among eight disjunct colonies in the eastern Swiss Alps. Elevated March to May temperatures, causing premature melting of Alpine snowcover, earlier plant phenology and subsequent improvement of ibex food resources, fuelled annual horn growth. These results reveal dependency of local trophic interactions on large‐scale climate dynamics, and provide evidence that declining herbivore performance is not a universal response to global warming even for high‐altitude populations that are also harvested.     

Sustainability of forest bioenergy in Europe: land-use-related carbon dioxide emissions of forest harvest residues

Increasing bioenergy production from forest harvest residues decreases litter input to the soil and can thus reduce the carbon stock and sink of forests. This effect may negate greenhouse gas savings obtained by using bioenergy. We used a spatially explicit modelling framework to assess the reduction in the forest litter and soil carbon stocks across Europe, assuming that a sustainable potential of bioenergy from forest harvest residues is taken into use. The forest harvest residue removal reduced the carbon stocks of litter and soil on average by 3% over the period from 2016 to 2100. The reduction was small compared to the size of the carbon stocks but significant in comparison to the amount of energy produced from the residues. As a result of these land-use-related emissions, bioenergy production from forest harvest residues would need to be continued for 60–80 years to achieve a 60% carbon dioxide (CO₂) emission reduction in heat and power generation compared to the fossil fuels it replaces in most European countries. The emission reductions achieved and their timings varied among countries because of differences in the litter and soil carbon loss. Our results show that extending the current sustainability requirements for bioliquids and biofuels to solid bioenergy does not guarantee efficient reductions in greenhouse gas emissions in the short-term. In the longer-term, bioenergy from forest harvest residues may pave the way to low-emission energy systems.     

Effects of social isolation on aggressiveness in fish with special reference to the swordtail (Xiphophorus helleri)

The attack readiness of socially isolated male swordtails ($\text{Xiphophorus helleri}$) was measured in two different aggression tests: (a) In the standard–opponent test the aggressive responses to a small, rather passive opponent swimming in a small adjacent compartment of the test aquarium were counted. (b) In the mirror test the subjects were confronted with their own mirror image. Social isolation for 4 weeks resulted in a decrease of attack readiness in both test situations. It is concluded that -- similar to cichlids -- external stimuli from conspecifics are essential for maintaining the level of aggression readiness characteristic for socially living males. There are good reasons to propose that the effect of external stimuli is mediated by the pituitary-gonadal axis. On the other hand, it is well known from previous studies that, in escalated encounters between freely swimming males, isolated males fight longer and at higher intensities for rank-order position than non-isolated males. The hypothesis is proposed that the high fighting intensity of previously isolated males could be due to an experience levelling effect of social isolation, i.e. the influence of different agonistic experience is reduced by isolation.A critical review of the literature on isolation-induced decremental and incremental effects on aggression in teleosts is presented. Often it is extremely difficult to compare the results of different authors because the methods of behavioural measurement differ to a large extent. However, it is a striking fact that social isolation of immature fish in all known cases has resulted in an increase of aggressiveness. Probably in mature males, depending on species and circumstances, either an incremental or a decremental effect of social isolation may be adaptive. On the one hand, a spontaneous increase of attack readiness may be advantageous for defence of a territory or a position in the social hierarchy and improves the ability of a single individual to join a group of strange conspecifics. On the other hand, it may be economic to lower the level of androgenic hormones to some extent in the absence of conspecifics, and this could lead to a reduction of the aggression level.