A global assessment of forest surface albedo and its relationships with climate and atmospheric nitrogen deposition

We present a global assessment of the relationships between the short‐wave surface albedo of forests, derived from the MODIS satellite instrument product at 0.5° spatial resolution, with simulated atmospheric nitrogen deposition rates (N_dep), and climatic variables (mean annual temperature T_m and total annual precipitation P), compiled at the same spatial resolution. The analysis was performed on the following five forest plant functional types (PFTs): evergreen needle‐leaf forests (ENF); evergreen broad‐leaf forests (EBF); deciduous needle‐leaf forests (DNF); deciduous broad‐leaf forests (DBF); and mixed‐forests (MF). Generalized additive models (GAMs) were applied in the exploratory analysis to assess the functional nature of short‐wave surface albedo relations to environmental variables. The analysis showed evident correlations of albedo with environmental predictors when data were pooled across PFTs: T_m and N_dep displayed a positive relationship with forest albedo, while a negative relationship was detected with P. These correlations are primarily due to surface albedo differences between conifer and broad‐leaf species, and different species geographical distributions. However, the analysis performed within individual PFTs, strengthened by attempts to select ‘pure’ pixels in terms of species composition, showed significant correlations with annual precipitation and nitrogen deposition, pointing toward the potential effect of environmental variables on forest surface albedo at the ecosystem level. Overall, our global assessment emphasizes the importance of elucidating the ecological mechanisms that link environmental conditions and forest canopy properties for an improved parameterization of surface albedo in climate models.     

A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry

Molecular beacons are dual-labelled probes that are typically used in real-time PCR assays, but have also been conjugated with solid matrices for use in microarrays or biosensors. We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. For this array system, molecular beacons were conjugated with microspheres using a biotin-streptavidin linkage. A bridged conjugation method using streptavidin increased the signal-to-noise ratio, allowing for further discrimination of target quantitation. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. Considering that routine flow cytometers are able to detect up to four fluorescent channels, this novel assay may allow for the specific multiplex detection of a nucleic acid panel in a single tube.     

Fraying around the edges: negative effects of the invasive Tradescantia zebrina Hort. ex Bosse (Commelinaceae) on tree regeneration in the Atlantic Forest under different competitive and environmental conditions

Aims Invasive plants modify the structure and functioning of natural environments and threat native plant communities. Invasive species are often favored by human interference such as the creation of artificial forest edges. Field removal experiments may clarify if invasive plants are detrimental to native plant regeneration and how this is related to other local factors. We assessed the joint effect of environment and competition with the invasiveTradescantia zebrinaon tree species recruitment in an Atlantic Forest fragment.     

Body proportions,microhabitat selection,and adaptive radiation of Liolaemus lizards in central Chile

Summary A biometric analysis of body proportions with presumably functional meaning for microhabitat selection was made on 12 species of Liolaemus lizards in central Chile. Characters studied were forelimb length, hindlimb length, tail length (all standardized by the corresponding snout-vent length), and the ratio forelimb/hindlimb length. It is shown that irrespective of terrestrial, saxicolous, or arboreal habits, Liolaemus species are remarkably similar in body proportions. The only exceptions are: L. lemniscatus, an open ground-dweller which exhibits significantly shorter limbs; and L. chiliensis and L. schroederi, both shrub-climbers which exhibit significantly longer tail. It is concluded that the adaptive radiation of Liolaemus lizards in central Chile has been accomplished mainly by diversification of activity time, food size, and microhabitat type. Morphological divergence in body proportions seems to have played an unimportant role.     

Chromosome segregation during female meiosis in C. elegans: A tale of pushing and pulling

The role of the kinetochore during meiotic chromosome segregation in C. elegans oocytes has been a matter of controversy. Danlasky et al. (2020. J. Cell. Biol. https://doi.org/10.1083/jcb.202005179) show that kinetochore proteins KNL-1 and KNL-3 are required for early stages of anaphase during female meiosis, suggesting a new kinetochore-based model of chromosome segregation.

Meiosis consists of two consecutive chromosome segregation events preceded by a single round of DNA replication. Homologous chromosomes are separated in meiosis I, which is followed by sister chromatid separation in meiosis II to produce haploid gametes. Both of these stages require chromosomes/chromatids to align during metaphase before separating to opposite poles during anaphase. During mitosis, microtubules emanating from centrosomes at opposite poles of the cell bind chromosomes through a multiprotein complex called the kinetochore, allowing chromosomes to be pulled apart (1, 2). This segregation event takes place in two stages: anaphase A, where chromosomes are pulled toward spindle poles due to microtubule depolymerization, and anaphase B, where spindle poles themselves move farther apart, taking the attached chromosomes with them (3, 4). In many organisms, including mammals, oocytes lack centrosomes, and it has been of great interest to clarify the mechanisms used to ensure chromosomes are properly segregated during female meiosis (5, 6). Caenorhabditis elegans has served as a model for studying both mitosis and meiosis, but the mechanisms operating during female meiosis have been a matter of debate and controversy.In 2010, Dumont et al. showed that the kinetochore is required for chromosome alignment and congression during metaphase (7). However, they suggested that chromosome segregation was the result of microtubule polymerization between the segregating chromosomes (Fig. 1), resulting in a pushing force exerted onto chromosomes toward the spindle poles in a largely kinetochore-independent manner (7). This mechanism was also supported by the finding that CLIP-associated protein (CLASP)–dependent microtubule polymerization between the segregating chromosomes is essential for chromosome separation (8). An alternative model suggested that chromosomes are transported through microtubule-free channels toward the spindle poles by the action of dynein (9). Later evidence put in doubt a role for dynein and favored a model in which chromosomes initially separate when the spindle shortens and the poles overlap with chromosomes in an anaphase A–like mechanism. This is then followed by separation of chromosome-bound poles by outward microtubule sliding in an anaphase B–like fashion (10). However, because microtubules emanating from the spindle poles are not required to separate the homologous chromosomes but microtubules between the separating chromosomes are (8), this model is unlikely, at least as an explanation for mid-/late-anaphase movement. Furthermore, although lateral microtubule interactions with chromosomes predominate during metaphase of C. elegans oocyte meiosis, cryo-electron tomography data described end-on attachments between the separating chromosomes as anaphase progresses (11). This led to the suggestion that lateral microtubule interactions with chromosomes are responsible for the initial separation, but microtubule polymerization between the separating chromosomes is required for the later stages of segregation (11). The mechanisms involved in this initial separation have remained obscure. In this issue, Danlasky et al. show that the kinetochore is in fact required for the initial stages of chromosome segregation during female meiosis—an important step forward in our understanding of the mechanisms governing acentrosomal chromosome segregation (12).Open in a separate windowFigure 1.Some of the key findings in Danlasky et al. Kinetochore proteins surround the outer surface of the chromosomes, resulting in a characteristic cup shape. As anaphase progresses, chromosomes come into close contact to the spindle poles (anaphase A). Chromosome stretching is provided by KNL-1, MIS-12 (KNL-3), and NDC-80 (KMN)–dependent forces. Once the spindle starts elongating (anaphase B), central spindle microtubules provide the pushing forces for chromosome segregation. At this stage, kinetochore proteins also occupy the inward face of separating chromosomes. Upon KMN network depletion, bivalents flatten, and chromosome congression and alignment are defective. Anaphase A chromosome movement is almost absent, which leads to error-prone anaphase B.By simultaneously depleting kinetochore proteins KNL-1 and KNL-3 in C. elegans, Danlasky et al. observed the meiotic chromosome congression and alignment defects described in previous studies (7). However, this double-depletion phenotype displayed three key characteristics that suggested a role for kinetochores in chromosome segregation, which are discussed below.The kinetochore is required for bivalent stretching. It was previously shown that the bivalent chromosomes stretch before the initiation of segregation (10). Danlasky et. al found that this stretching of the chromosomes did not occur when KNL-1,3 were depleted, indicating that the kinetochore is required for this process (Fig. 1). Together with the observation that kinetochore proteins appear to extend toward the spindle poles, this finding suggested that pulling forces resulting from the interaction between the kinetochore and spindle microtubules are occurring during metaphase/preanaphase (Fig. 1).The kinetochore is required for anaphase A. In C. elegans female meiosis, anaphase A occurs when homologous chromosomes begin to separate during spindle shortening, and anaphase B when the chromosomes separate alongside the spindle poles (10). Danlasky et al. observed that KNL-1,3 depletion drastically reduced the velocity of anaphase A, as chromosomes only separated when spindle poles began to move apart. This indicated that pulling forces caused by the interaction between the kinetochore and spindle microtubules are also important for the initial separation of homologous chromosomes in anaphase A.The kinetochore is required for proper separation of homologous chromosomes. In KNL-1,3 depletion strains, 60% of bivalents failed to separate before segregation began, resulting in intact bivalents being pulled to the same spindle pole (Fig. 1). This failure of homologous chromosomes to separate was not thought to be a result of KNL-1,3 depletion interfering with the cleavage of cohesin that holds the two homologous chromosomes together because (a) separase and AIR-2^AuroraB, both of which are required for cohesin cleavage, localized normally during metaphase and anaphase, and (b) bivalents separated by metaphase II. This leaves the possibility open that the failure of bivalents to separate was due to the disrupted pulling forces thought to be important in bivalent stretching and anaphase A.Altogether, these data strongly indicate that the kinetochore is required not only for chromosome congression and alignment but also for the early stages of homologue separation. Anaphase B occurred successfully in the absence of KNL-1,3 but was more error prone, likely as a result of the earlier congression and anaphase A defects. While it is clear that chromosome masses do segregate in the absence of the kinetochore, this segregation is highly erroneous as a result of defects during the earlier stages of segregation in anaphase A (Fig. 1).The findings of Danlasky et al. raise testable hypotheses that could significantly enhance our understanding of acentrosomal chromosome segregation. Further investigation of the proposed pulling forces required during metaphase and early anaphase will be of great interest. Additionally, a more detailed analysis of the dynamic localization of separase and Securin, as well as assessing successful cohesin cleavage when KNL-1,3 are depleted, would back up the assertion that the failure of homologous chromosomes to separate was not due to the kinetochore impacting cohesin cleavage. It has previously been shown that the CLASP orthologue CLS-2 in C. elegans localizes to the kinetochore surrounding the bivalent chromosomes during metaphase before relocalizing to the central spindle during anaphase (7, 8, 13). It will be interesting to examine whether this key microtubule-stabilizing protein contributes to anaphase A pulling forces alongside its essential role in microtubule polymerization between chromosomes in anaphase B (8).While the regulation of proper chromosome segregation during acentrosomal meiosis in C. elegans is not yet fully understood, Danlasky et al.’s results represent a significant step forward in this endeavor by showing that the kinetochore is in fact required for the early stages of chromosome segregation.     

Revisiting the coupling of fatty acid to phospholipid synthesis in bacteria with FapR regulation

A key aspect in membrane biogenesis is the coordination of fatty acid to phospholipid synthesis rates. In most bacteria, PlsX is the first enzyme of the phosphatidic acid synthesis pathway, the common precursor of all phospholipids. Previously, we proposed that PlsX is a key regulatory point that synchronizes the fatty acid synthase II with phospholipid synthesis in Bacillus subtilis. However, understanding the basis of such coordination mechanism remained a challenge in Gram-positive bacteria. Here, we show that the inhibition of fatty acid and phospholipid synthesis caused by PlsX depletion leads to the accumulation of long-chain acyl-ACPs, the end products of the fatty acid synthase II. Hydrolysis of the acyl-ACP pool by heterologous expression of a cytosolic thioesterase relieves the inhibition of fatty acid synthesis, indicating that acyl-ACPs are feedback inhibitors of this metabolic route. Unexpectedly, inactivation of PlsX triggers a large increase of malonyl-CoA leading to induction of the fap regulon. This finding discards the hypothesis, proposed for B. subtilis and extended to other Gram-positive bacteria, that acyl-ACPs are feedback inhibitors of the acetyl-CoA carboxylase. Finally, we propose that the continuous production of malonyl-CoA during phospholipid synthesis inhibition provides an additional mechanism for fine-tuning the coupling between phospholipid and fatty acid production in bacteria with FapR regulation.     

Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

DNA methylation can be environmentally modulated and plays a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) were assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability was positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.     

Scaling-up of a B-phycoerythrin production and purification bioprocess involving aqueous two-phase systems: Practical experiences

One of the most attractive segments in food and cosmetic industries is that of natural pigments. Since some synthetic pigments have been reported to be hazardous for humans, natural pigments obtained through biotechnological processes represent an attractive alternative. Our research group has previously worked on the development of an aqueous two-phase system (ATPS)-based prototype process for the recovery of B-phycoerythrin (BPE), a natural high-value pigment obtained from Porphyridium cruentum. Detailed studies describing the scaling up of ATPS processes from bench scale to pilot plant facilities are not common. In this paper experiences derived from the scale-up of a previously developed process for production and recovery of highly purified (purity defined as the absorbance ratio A₅₄₅/A₂₈₀ > 4) BPE are described, where a scale-up factor of 850× was implemented. Characterization of cell disruption with a pilot-scale bead mill allowed efficient BPE release at 2900 rpm, 10% (w/v) sample load, 60% (v/v) bead load and 0.5 mm glass beads and 22 min of residence time with a yield of 1.35 mg BPE/g of wet biomass. BPE was recovered and purified using a strategy comprising isoelectric precipitation, aqueous two-phase fractionation and ultrafiltration. A 54% global BPE recovery yield, with final purity of 4.1, was achieved under optimal process conditions. Considering total costs for raw materials and energy expenditures for one batch, it was determined that the production cost of BPE was of $1.17 USD/mg, which is underneath the commercial price of a BPE standard (>$30 USD/mg).     

A structural modeling approach for the understanding of initiation and elongation of ALS-linked superoxide dismutase fibrils

Familial amyotrophic lateral sclerosis caused by mutations in copper-zinc superoxide dismutase (SOD1) is characterized by the presence of SOD1-rich inclusions in spinal cords. It has been shown that a reduced intra-subunit disulfide bridge apo-SOD1 can rapidly initiate fibrillation forming an inter-subunits disulfide under mild, physiologically accessible conditions. Once initiated, elongation can proceed via recruitment of either apo or partially metallated disulfide-intact SOD1 and the presence of copper, but not zinc, ions inhibit fibrillation. We propose a structural model, refined through molecular dynamics simulations, that, taking into account these experimental findings, provides a molecular explanation for the initiation and the elongation of SOD1 fibrils in physiological conditions. The model indicates the occurrence of a new dimeric unit, prone to interact one with the other due to the presence of a wide hydrophobic surface and specific electrostatic interactions. The model has dimensions consistent with the SOD1 fibril size observed through electron microscopy and provides a structural basis for the understanding of SOD1 fibrillation.

Somatic Mutations in Exocrine Pancreatic Tumors: Association with Patient Survival

KRAS mutations are major factors involved in initiation and maintenance of pancreatic tumors. The impact of different mutations on patient survival has not been clearly defined. We screened tumors from 171 pancreatic cancer patients for mutations in KRAS and CDKN2A genes. Mutations in KRAS were detected in 134 tumors, with 131 in codon 12 and only 3 in codon 61. The GGT>GAT (G12D) was the most frequent mutation and was present in 60% (80/134). Deletions and mutations in CDKN2A were detected in 43 tumors. Analysis showed that KRAS mutations were associated with reduced patient survival in both malignant exocrine and ductal adenocarcinomas (PDAC). Patients with PDACs that had KRAS mutations showed a median survival of 17 months compared to 30 months for those without mutations (log-rank P = 0.07) with a multivariate hazard ratio (HR) of 2.19 (95%CI 1.09–4.42). The patients with G12D mutation showed a median survival of 16 months (log-rank-test P = 0.03) and an associated multivariate HR 2.42 (95%CI 1.14–2.67). Although, the association of survival in PDAC patients with CDKN2A aberrations in tumors was not statistically significant, the sub-group of patients with concomitant KRAS mutations and CDKN2A alterations in tumors were associated with a median survival of 13.5 months compared to 22 months without mutation (log-rank-test P = 0.02) and a corresponding HR of 3.07 (95%CI 1.33–7.10). Our results are indicative of an association between mutational status and survival in PDAC patients, which if confirmed in subsequent studies can have potential clinical application.