THE SYSTEMATICS OF THE BURROWING WATER BEETLES (COLEOPTERA: ADEPHAGA: NOTERIDAE)

The aquatic beetle family Noteridae (Coleoptera: Adephaga) comprises a group with poorly studied diversity that has received limited systematic study. Despite the corroboration of multiple phylogenic reconstructions, many relationships within Noteridae remain poorly supported or unresolved. Here I address the questions surrounding the systematics of Noteridae in three ways. First, a review of previously constructed noterid phylogenies is presented and methods, variation in recovered relationships and the current classification of Noteridae are explored. Second, a phylogeny of Noteridae is inferred based on the analysis of DNA sequence data of five gene fragments: COI, H3, 16S, 18S, and 28S. Our taxon sampling of Noteridae is the most robust of any phylogenetic investigation of Noteridae to date and includes representatives for 16 of the 17 current noterid genera. Bayesian and Maximum likelihood analyses produce highly supported trees that strongly contradict previous studies. Our results recover the monophyly of the following higher level groups: (1). Meruidae + Noteridae, though the exact nature of this relationship is unresolved; (2) Phreatodytinae + Notomicrinae; and (3) Noterinae. All known genera are found to be monophyletic except Hydrocanthus Say, found paraphyletic with respect to Mesonoterus Sharp and Prionohydrus Gomez & Miller, and Suphisellus Crotch, found to be paraphyletic with respect to Pronoterus. Thus the following changes in classification and taxonomy are proposed: the subgenus Sternocanthus Guignot is resurrected from synonymy stat. rev. and elevated to the genus rank stat. n. to contain Old World members of the genus Hydrocanthus sensu lato; and Pronoterus Sharp syn. n. is placed in synonymy with Suphisellus Crotch. All tribes within the Noterinae are recovered as paraphyletic or invalid due to synonymy and the a revised classification is thus proposed: (1) Noterini Thomson sensu n. is redefined contain the genera Noterus Clairville and Neohydrocoptus Satô, thus including Neohydrocoptini Zalat et al. syn. n. as a junior synonym ;(2) Tonerini Miller sensu n. is redefined to hold the genera Synchortus Sharp, Tonerus Miller, and Liocanthydrus Guignot; (4) Renotini trib. n. is erected to contain the genus Renotus Guignot; (5) Suphisini Sharp rev. stat. is resurrected from synonymy to hold the genera Suphis Aubé, Canthysellus Baca & Toledo gen. n., Suphisellus Crotch incl. Pronoterus Sharp, and a tentative new noterid genus; and (6) Hydrocanthini Sharp stat. rev. is resurrected from synonymy to hold the genera Canthydrus Sharp, Sternocanthus Guignot, Hydrocanthus Say, Mesonoterus Sharp and Prionohydrus Gomez & Miller. A discussion of relationships, classification and morphology is presented. Finally, the poor documentation of noterid diversity is addressed with the description of the genus Canthysellus Baca & Toledo gen. n., here erected to contain three species Canthysellus buqueti (Laporte, 1835), C. sipaliwini sp. n. and C. peruanus sp. n. Descriptions, diagnoses, illustrations of diagnostic characters and a key to species of Canthysellus are provided

The enduring value of reciprocal illumination in the era of insect phylogenomics: a response to Cai et al. (2020)

Arguably no other group within Coleoptera has received as robust and sustained investigation into their phylogenetic relationships as aquatic beetles. Among this ecological guild, evolutionary relationships of the families within Dytiscoidea, a clade comprising the charismatic diving beetles (Dytiscidae) and their close relatives, have received particular attention. Very recently, four different studies were published investigating the phylogeny of Dytiscoidea, three of which utilized phylogenomic data, the most recent by Cai etal. (2020). Cai et al. (2020) (hereafter CEA) approached investigating theevolutionary relationships among dytiscoid families by reanalysing the transcriptomic dataset of Vasilikopoulos et al. (2019) using different evolutionary models and data trimming regimes. CEAs analyses recovered three different topologies for relationships amongst Dytiscoidea, two of which have been recovered in several previous studies. The primary difference among these topologies is the placement of Hygrobiidae, either as sister to (Dytiscidae (Amphizoidae + Aspidytidae)), sister to Amphizoidae + Aspidytidae, or as sister to Dytiscidae. In CEA, topologies shown in Fig. 1A, C both received maximal (e.g. bootstrap values of 100 and posterior probabilities of 100%) to strong support respectively via their preferred model of evolution. Whereas CEAs recovery of Hygrobiidae sister to Amphizoidae + Aspidytidae was not as strongly supported, Gustafson et al. (2020) recovered this topology primarily with strong to maximal support across all analyses with comprehensive taxon sampling of Dytiscoidea. Rather than treating the three topologies recovered both within their own study and elsewhere as equally viable hypotheses, CEA dismissed the relationships shown in Fig. 1A, B as the result of phylogenetic methodological error, promoting Fig. 1C as their preferred tree because it is consistent with morphology-based views of dytiscoid relationships. Here, we address (i) the manner in which CEA approached reconciling conflicting hypotheses about the evolution of Dytiscoidea; and (ii) the misconception that dytiscoid relationships shown in Fig. 1C are the most consistent with morphology-based views in relation to those of Fig. 1A, B.Fil: Gustafson, Grey T.. University of Kansas; Estados UnidosFil: Miller, Kelly B.. University of New Mexico. Department of Biology; Estados UnidosFil: Michat, Mariano Cruz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Alarie, Yves. Laurentian University. Department of Biology; CanadáFil: Baca, Stephen M.. University of Kansas; Estados UnidosFil: Balke, Michael. Zoologische Staatssammlung Munchen; AlemaniaFil: Short, Andrew E. Z.. University of Kansas; Estados Unido

Crop modelling: towards locally relevant and climate-informed adaptation

A gap between the potential and practical realisation of adaptation exists: adaptation strategies need to be both climate-informed and locally relevant to be viable. Place-based approaches study local and contemporary dynamics of the agricultural system, whereas climate impact modelling simulates climate-crop interactions across temporal and spatial scales. Crop-climate modelling and place-based research on adaptation were strategically reviewed and analysed to identify areas of commonality, differences, and potential learning opportunities to enhance the relevance of both disciplines through interdisciplinary approaches. Crop-modelling studies have projected a 7–15% mean yield change with adaptation compared to a non-adaptation baseline (Nature Climate Change 4:1–5, 2014). Of the 17 types of adaptation strategy identified in this study as place-based adaptations occurring within Central America, only five were represented in crop-climate modelling literature, and these were as follows: fertiliser, irrigation, change in planting date, change in cultivar and area cultivated. The breath and agency of real-life adaptation compared to its representation in modelling studies is a source of error in climate impact simulations. Conversely, adaptation research that omits assessment of future climate variability and impact does not enable to provide sustainable adaptation strategies to local communities so risk maladaptation. Integrated and participatory methods can identify and reduce these sources of uncertainty, for example, stakeholder’s engagement can identify locally relevant adaptation pathways. We propose a research agenda that uses methodological approaches from both the modelling and place-based approaches to work towards climate-informed locally relevant adaptation

The Interferon Response Inhibits HIV Particle Production by Induction of TRIM22

Treatment of human cells with Type 1 interferons restricts HIV replication. Here we report that the tripartite motif protein TRIM22 is a key mediator. We used transcriptional profiling to identify cellular genes that were induced by interferon treatment and identified TRIM22 as one of the most strongly up-regulated genes. We confirmed, as in previous studies, that TRIM22 over-expression inhibited HIV replication. To assess the role of TRIM22 expressed under natural inducing conditions, we compared the effects of interferon in cells depleted for TRIM22 using RNAi and found that HIV particle release was significantly increased in the knockdown, implying that TRIM22 acts as a natural antiviral effector. Further studies showed that TRIM22 inhibited budding of virus-like particles containing Gag only, indicating that Gag was the target of TRIM22. TRIM22 did not block the release of MLV or EIAV Gag particles. Inhibition was associated with diffuse cytoplasmic staining of HIV Gag rather than accumulation at the plasma membrane, suggesting TRIM22 disrupts proper trafficking. Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 antiviral activity. These data disclose a pathway by which Type 1 interferons obstruct HIV replication

Immunisation with Recombinant PfEMP1 Domains Elicits Functional Rosette-Inhibiting and Phagocytosis-Inducing Antibodies to Plasmodium falciparum

BACKGROUND: Rosetting is a Plasmodium falciparum virulence factor implicated in the pathogenesis of life-threatening malaria. Rosetting occurs when parasite-derived P. falciparum Erythrocyte Membrane Protein One (PfEMP1) on the surface of infected erythrocytes binds to human receptors on uninfected erythrocytes. PfEMP1 is a possible target for a vaccine to induce antibodies to inhibit rosetting and prevent severe malaria. METHODOLOGY/FINDINGS: We examined the vaccine potential of the six extracellular domains of a rosette-mediating PfEMP1 variant (ITvar9/R29var1 from the R29 parasite strain) by immunizing rabbits with recombinant proteins expressed in E. coli. Antibodies raised to each domain were tested for surface fluorescence with live infected erythrocytes, rosette inhibition and phagocytosis-induction. Antibodies to all PfEMP1 domains recognized the surface of live infected erythrocytes down to low concentrations (0.02-1.56 µg/ml of total IgG). Antibodies to all PfEMP1 domains except for the second Duffy-Binding-Like region inhibited rosetting (50% inhibitory concentration 0.04-4 µg/ml) and were able to opsonize and induce phagocytosis of infected erythrocytes at low concentrations (1.56-6.25 µg/ml). Antibodies to the N-terminal region (NTS-DBL1α) were the most effective in all assays. All antibodies were specific for the R29 parasite strain, and showed no functional activity against five other rosetting strains. CONCLUSIONS/SIGNIFICANCE: These results are encouraging for vaccine development as they show that potent antibodies can be generated to recombinant PfEMP1 domains that will inhibit rosetting and induce phagocytosis of infected erythrocytes. However, further work is needed on rosetting mechanisms and cross-reactivity in field isolates to define a set of PfEMP1 variants that could induce functional antibodies against a broad range of P. falciparum rosetting parasites

Timing Constraints of In Vivo Gag Mutations during Primary HIV-1 Subtype C Infection

Background: Aiming to answer the broad question “When does mutation occur?” this study examined the time of appearance, dominance, and completeness of in vivo Gag mutations in primary HIV-1 subtype C infection. Methods: A primary HIV-1C infection cohort comprised of 8 acutely and 34 recently infected subjects were followed frequently up to 500 days post-seroconversion (p/s). Gag mutations were analyzed by employing single-genome amplification and direct sequencing. Gag mutations were determined in relation to the estimated time of seroconversion. Time of appearance, dominance, and completeness was compared for different types of in vivo Gag mutations. Results: Reverse mutations to the wild type appeared at a median (IQR) of 62 (44;139) days p/s, while escape mutations from the wild type appeared at 234 (169;326) days p/s (p<0.001). Within the subset of mutations that became dominant, reverse and escape mutations appeared at 54 (30;78) days p/s and 104 (47;198) days p/s, respectively (p<0.001). Among the mutations that reached completeness, reverse and escape mutations appeared at 54 (30;78) days p/s and 90 (44;196) days p/s, respectively (p = 0.006). Time of dominance for reverse mutations to and escape mutations from the wild type was 58 (44;105) days p/s and 219 (90;326) days p/s, respectively (p<0.001). Time of completeness for reverse and escape mutations was 152 (100;176) days p/s and 243 (101;370) days p/s, respectively (p = 0.001). Fitting a Cox proportional hazards model with frailties confirmed a significantly earlier time of appearance (hazard ratio (HR): 2.6; 95% CI: 2.3–3.0), dominance (4.8 (3.4–6.8)), and completeness (3.6 (2.3–5.5)) of reverse mutations to the wild type Gag than escape mutations from the wild type. Some complex mutational pathways in Gag included sequential series of reversions and escapes. Conclusions: The study identified the timing of different types of in vivo Gag mutations in primary HIV-1 subtype C infection in relation to the estimated time of seroconversion. Overall, the in vivo reverse mutations to the wild type occurred significantly earlier than escape mutations from the wild type. This shorter time to incidence of reverse mutations remained in the subsets of in vivo Gag mutations that reached dominance or completeness

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases

Measurement of inclusive jet and dijet cross-sections in proton-proton collisions at s √ =13 TeV with the ATLAS detector

Inclusive jet and dijet cross-sections are measured in proton-proton collisions at a centre-of-mass energy of 13 TeV. The measurement uses a dataset with an integrated luminosity of 3.2 fb−1 recorded in 2015 with the ATLAS detector at the Large Hadron Collider. Jets are identified using the anti-kt algorithm with a radius parameter value of R = 0.4. The inclusive jet cross-sections are measured double-differentially as a function of the jet transverse momentum, covering the range from 100 GeV to 3.5 TeV, and the absolute jet rapidity up to |y| = 3. The double-differential dijet production cross-sections are presented as a function of the dijet mass, covering the range from 300 GeV to 9 TeV, and the half absolute rapidity separation between the two leading jets within |y| < 3, y∗, up to y∗ = 3. Next-to-leading-order, and next-to-next-to-leading-order for the inclusive jet measurement, perturbative QCD calculations corrected for non-perturbative and electroweak effects are compared to the measured cross-sections

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology