Viruses present an amazing genetic variability. An ensemble of infecting viruses, also called a viral quasispecies, is a cloud of mutants centered around a specific genotype. The simplest model of evolution, whose equilibrium state is described by the quasispecies equation, is the Moran–Kingman model. For the sharp-peak landscape, we perform several exact computations and derive several exact formulas. We also obtain an exact formula for the quasispecies distribution, involving a series and the mean fitness. A very simple formula for the mean Hamming distance is derived, which is exact and does not require a specific asymptotic expansion (such as sending the length of the macromolecules to $\infty$ or the mutation probability to 0). With the help of these formulas, we present an original proof for the well-known phenomenon of the error threshold. We recover the limiting quasispecies distribution in the long-chain regime. We try also to extend these formulas to a general fitness landscape. We obtain an equation involving the covariance of the fitness and the Hamming class number in the quasispecies distribution. Going beyond the sharp-peak landscape, we consider fitness landscapes having finitely many peaks and a plateau-type landscape. Finally, within this framework, we prove rigorously the possible occurrence of the survival of the flattest, a phenomenon which was previously discovered by Wilke et al. (Nature 412, 2001) and which has been investigated in several works (see e.g. Codoñer et al. (PLOS Pathogens 2, 2006), Franklin et al. (Artificial Life 25, 2019), Sardanyés et al. (J. Theoret. Biol. 250, 2008), and Tejero et al. (BMC Evolutionary Biol. 11, 2011)).

The Galician definite article and direct object clitics exhibit allomorphy-like alternations which raise a number of questions for the morphology-phonology interface. This squib highlights inadequacies of allomorphic approaches to these alternations, outlining a novel way forward in which segmental changes apply to a stem in a fashion reminiscent of Celtic mutation. Differences between the article and the object clitic can then be ascribed to their prosodic weights, evident elsewhere in the language. Taken together, these findings expand our view of potential triggers for morphophonological alternations.

Danon disease is a rare X-linked disorder caused by deficiency of the lysosome-associated membrane protein-2. We report a case of hypertrophic obstructive cardiomyopathy secondary to a novel mutation in the lysosome-associated membrane protein-2 gene in a 10-year-old male adolescent. We performed a modified extended Morrow procedure to minimise the risk of death and improve the patient’s quality of life. The patient did not have exertional dyspnoea, and auscultation did not reveal a cardiac murmur at 1-year follow-up.

We establish some properties of $\tau$-exceptional sequences for finite-dimensional algebras. In an earlier paper, we established a bijection between the set of ordered support $\tau$-tilting modules and the set of complete signed $\tau$-exceptional sequences. We describe the action of the symmetric group on the latter induced by its natural action on the former. Similarly, we describe the effect on a $\tau$-exceptional sequence obtained by mutating the corresponding ordered support $\tau$-tilting module via a construction of Adachi-Iyama-Reiten.

We consider a spatial model of cancer in which cells are points on the d-dimensional torus $\mathcal{T}=[0,L]^d$, and each cell with $k-1$ mutations acquires a kth mutation at rate $\mu_k$. We assume that the mutation rates $\mu_k$ are increasing, and we find the asymptotic waiting time for the first cell to acquire k mutations as the torus volume tends to infinity. This paper generalizes results on waiting for $k\geq 3$ mutations in Foo et al. (2020), which considered the case in which all of the mutation rates $\mu_k$ are the same. In addition, we find the limiting distribution of the spatial distances between mutations for certain values of the mutation rates.

Abnormal embryonic development may result from mutations caused by genetics, environmental conditions or viruses. This study reports cases of cyclopia and a mouth malformation in two embryonic blue shark Prionace glauca collected off southern Brazil (South-western Atlantic). Such malformations are likely to reduce the chances of survival of embryos and neonates.

Acetolactate synthase (ALS) inhibitors provide postemergence control of green kyllinga (Kyllinga brevifolia Rottb.) in turfgrass and other cropping systems. A suspected resistant (R) biotype of K. brevifolia was collected from a golf course and evaluated for resistance to ALS inhibitors. In greenhouse experiments, the sulfosulfuron rates required to cause 50% shoot biomass reduction from the nontreated at 4 wk after treatment (WAT) were 10 and 792 g ai ha−1 for the susceptible (S) and R biotypes, respectively. The rates required to cause 50% injury at 4 WAT were 189 and >3,360 g ai ha−1, respectively. In other experiments, shoot mass of the R biotype was not reduced by imazaquin, trifloxysulfuron-sodium, pyrimisulfan, thiencarbazone + foramsulfuron + halosulfuron, florasulam + halauxifen-methyl, and bentazon compared with the nontreated, while sulfentrazone reduced biomass similarly for both R and S biotypes. Gene sequencing of the R biotype revealed a mutation at Asp-376-Glu that has previously conferred resistance to five families of ALS inhibitors. This is the first report of ALS-inhibitor resistance in K. brevifolia.

Dithiopyr and dinitroanilines are preemergence-applied, mitotic-inhibiting herbicides used to control goosegrass [Eleusine indica (L.) Gaertn.] in turfgrass. A suspected resistant E. indica population was collected from a golf course putting green and was evaluated for possible resistance to dithiopyr and prodiamine. After dose–response evaluation, the α-tubulin gene was sequenced for known target-site mutations that have been reported to confer resistance to mitotic-inhibiting herbicides. A mutation was discovered that resulted in an amino acid substitution at position 136 from leucine to phenylalanine (Leu-136-Phe). Previous research has indicated that Leu-136-Phe does confer resistance to dinitroaniline herbicides. The level of resistance indicated by regression models and I50 values indicates that there is 54.1-, 4.7-, >100-, and >100-fold resistance to dithiopyr, prodiamine, pendimethalin, and oryzalin, respectively, when compared with the susceptible population based on seedling emergence response and 88.4-, 7.8-, >100-, and >100-fold resistance to dithiopyr, prodiamine, pendimethalin, and oryzalin, respectively, when compared with the susceptible population based on biomass reduction response. This is the first report of less resistance to prodiamine compared with pendimethalin or oryzalin due to a target-site α-tubulin mutation and the first report of a target-site α-tubulin mutation associated with dithiopyr resistance.

Noonan syndrome is a genetic disorder characteried by short stature, typical facial features, developmental delay, and CHD. In this single-centre retrospective study, we analysed typical Noonan syndrome-related electrocardiographic features in 95 patients with clinically and molecularly confirmed Noonan syndrome. Typical Noonan syndrome-related electrocardiographic features are left axis deviation, small left precordial R-waves, large right precordial S-waves, abnormal Q-wave, and abnormal wide QRS complex. In this representative cohort, CHD was found in 59 patients (62.1%) and typical Noonan syndrome-related electrographic features in 60 patients (63.2%). The typical Noonan syndrome-related electrographic features were also increased over baseline in patients without CHD (41.7%). Of all 95 patients, left axis deviation was seen in 46.3%, small left precordial R-waves in 30.5%, large right precordial S-waves in 5.3%, and abnormal Q-wave and wide QRS complex in 2.1%. There was no significant difference in the frequency of the individual-specific electrographic features between the group with CHD and the group without CHD. However, there were significantly more patients with a small left precordial R-wave in the subgroup with pulmonary stenosis compared to patients without pulmonary stenosis. Conclusion: Specific Noonan syndrome-related electrographic features are frequently present in patients with Noonan syndrome, also in the absence of CHD. These results suggest that there may be a continuum of cardiac anomalies from overt CHD to milder abnormalities that are only seen on electrocardiogram.

The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.

Redroot pigweed (Amaranthus retroflexus L.) is a dominant weed in soybean [Glycine max (L.) Merr.] fields in Heilongjiang Province, China. High selective pressure caused by the extensive application of the protoporphyrinogen oxidase (PPO)-inhibiting herbicide fomesafen has caused A. retroflexus to evolve resistance to this herbicide. Two susceptible and two resistant populations (S1, S2, R1, and R2) were selected in this study to illustrate the target-site resistance mechanism in resistant A. retroflexus. Whole-plant bioassays indicated that R1 and R2 had evolved high-level resistance to fomesafen, with resistance factors of 27.0 to 27.9. Sequence alignment of the PPO gene showed an Arg-128-Gly substitution in PPX2. The basal expression differences of PPX1 and PPX2 between the S1 and R1 plants were essentially nonsignificant, whereas the basal expression of PPX2 in R2 plants was slightly lower than in S1 plants. Compared with the PPX1 gene, the PPX2 gene maintained higher expression in the resistant plants after treatment with fomesafen. An enzyme-linked immunosorbent assay showed a similar basal PPO content between the susceptible and resistant plants without treatment. After fomesafen treatment, the PPO content decreased sharply in the susceptible plants compared with the resistant plants. Furthermore, after 24 h of treatment, the resistant plants showed increased PPO content, whereas the susceptible plants had died. The PPO2 mutation resulted in high extractable PPO activity and low sensitivity to fomesafen along with changes in PPO enzyme kinetics. Although the mutant PPO2 exhibited increased Km values in the resistant plants, the Vmax values in these plants were also increased. Changes in the properties of the PPO enzyme due to an Arg-128-Gly substitution in PPX2, including changes in enzyme sensitivity and enzyme kinetics, are the target-site mechanism of resistance in A. retroflexus.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused acute respiratory distress syndrome affecting more than 200 countries with varied mortality rate. Successive genetic variants of SARS-CoV-2 become evident across the globe immediately after its complete genome sequencing. Here, we found a decent association of SARS-CoV-2 ORF3a mutation with higher mortality rate. Extensive in silico studies revealed several amino acid changes in ORF3a protein which ultimately leads to diverse structural modifications like B cell epitope loss, gain/loss of phosphorylation site and loss of leucine zipper motif. We could further relate these changes to the enhanced antigenic diversity of SARS-CoV-2. Through protein−protein network analysis and functional annotation studies, we obtained a close federation of ORF3a protein with host immune response via divergent signal transduction pathways including JAK-STAT, chemokine and cytokine-related pathways. Our data not only unveil the fairly appreciable association of ORF3a mutation with higher mortality rate, but also suggest a potential mechanistic insight towards the immunopathogenic manifestation of SARS-CoV-2 infection.