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The vast majority of missense variants observed in the human genome are of unknown clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. By combining structural context and evolutionary conservation, our model achieves state-of-the-art results across a wide range of genetic and experimental benchmarks, all without explicitly training on such data. The average pathogenicity score of genes is also predictive for their cell essentiality, capable of identifying short essential genes that existing statistical approaches are underpowered to detect. As a resource to the community, we provide a database of predictions for all possible human single amino acid substitutions and classify 89% of missense variants as either likely benign or likely pathogenic.

The selection of sustainable crops adaptable to the rapidly changing environment, which also cater to the dietary needs of the growing population, is a primary challenge in meeting food security. Grains from ancient crops such as amaranth, quinoa, and millets are positioned to address this challenge and hence have gained dietary predominance among cereals and pseudocereals due to their nutritional value and energy efficiency. From a nutritional perspective, they are recognized for their complete protein, phenolic compounds and flavonoids, prebiotic fibers, and essential micronutrients, including minerals and vitamins. Bioactive peptides from their proteins have shown antihypertensive, antidiabetic, antioxidant, and anticancer properties. The nutritional diversity of these grains makes them a preferred choice over traditional cereals for developing healthy, sustainable food products such as plant-based dairy, vegan meats, and gluten-free products. With growing consumer awareness about sustainability and health, the categories mentioned above are transitioning from 'emerging' to 'mainstream'; however, there is still a significant need to include such healthy grains to fulfill the nutritional gap. This review article emphasizes the health benefits of amaranth, quinoa, and millet grains and discusses the recent research progress in understanding their application in new sustainable food categories. The challenges associated with their incorporation into novel foods and future research directions are also provided.

Cytogenetic analyses were performed on specimens of Leptodactylus bufonius from different localities in Argentina. Mitotic chromosomes were studied with Giemsa and differential staining techniques (Ag-NOR, C-banding, and CMA3/DAPI) and fluorescence in situ hybridization with the 18S DNAr probe. All specimens showed karyotypes with 2n = 2x = 22 and FN = 44. Secondary constrictions were present in the long arm of chromosome pair 8, coincident with Ag-NOR and hybridization signals of the 18S DNAr probe. The C-banding technique evidenced an important amount of heterochromatin with a sex-linked pericentromeric band in the short arm of chromosome pair 4. This heterochromatic band was heteromorphic in males but present in both homologues of females, and it was CMA3 positive (DAPI negative) at fluorescence staining. The occurrence of heteromorphic XY sex chromosomes in L. bufonius is the second known case in Leptodactylus and the fifth within the speciose family Leptodactylidae.

A new species of Leptodactylus frog (Anura: Leptodactylidae) from the South American Gran Chaco, morphologically similar and previously confused with the widespread Leptodactylus mystacinus , is described through the use of multiple sources of evidence (molecular, external morphology, coloration, osteology, bioacoustics, and behavior). The phylogenetic analysis with partial sequences of mitochondrial rDNA genes (12S and 16S) recovered the new species within the L. fuscus group, being highly divergent (>3% genetic distance in 16S). The new species was recovered as sister taxa of L. mystacinus , from which it is distinguished by tympanum coloration, cephalic index, dorsum and legs coloration, and some osteological differences in nasals and prevomers. This new frog is characterized by a moderate body size (SVL 46.80-66.21 mm), distinctive color pattern (reddish dorsal surfaces of body with noticeable black stripes in the dorsolateral folds), a circular and dark tympanum with dark tympanic annuli, and behavior of males that call on top of fallen logs and tree branches close to the ground., Competing Interests: The authors declare that they have no competing interests., (© 2019 Schneider et al.)

Misiones, Argentina, contains the largest remaining tract of Upper Paraná Atlantic Forest ecoregion; however, ~50% of native forest is unprotected and located in a mosaic of plantations, agriculture, and pastures. Existing protected areas are becoming increasingly isolated due to ongoing habitat modification. These factors, combined with lower than expected regional carnivore densities, emphasize the need to understand the effect of fragmentation on animal movement and connectivity between protected areas. Using detection dogs and genetic analyses of scat, we collected data on jaguars (Panthera onca), pumas (Puma concolor), ocelots (Leopardus pardalis), oncillas (Leopardus tigrinus), and bush dogs (Speothos venaticus) across habitats that varied in vegetation, disturbance, human proximity, and protective status. With MaxEnt we evaluated habitat use, habitat suitability, and potential species richness for the five carnivores across northern-central Misiones, Argentina. Through a multifaceted cost analysis that included unique requirements of each carnivore and varying degrees of overlap among them, we determined the optimal location for primary/secondary corridors that would link the northern-central zones of the Green Corridor in Misiones and identified areas within these corridors needing priority management. A secondary analysis, comparing these multispecies corridors with the jaguar's unique requirements, demonstrated that this multispecies approach balanced the preferences of all five species and effectively captured areas required by this highly restricted and endangered carnivore. We emphasize the potential importance of expanding beyond a single umbrella or focal species when developing biological corridors that aim to capture the varied ecological requirements of coexisting species and ecological processes across the landscape. Detection dogs and genetic analyses of scat allow data on multiple species to be collected efficiently across multiple habitat types independent of the degree of legal protection. These data used with multifocal GIS analyses balance the varying degree of overlap and unique properties among them allowing for comprehensive conservation strategies to be developed relatively rapidly. Our comprehensive approach serves as a model to other regions faced with habitat loss and lack of data. The five carnivores focused on in our study have wide ranges, so the results from this study can be expanded and combined with surrounding countries, with analyses at the species or community level.

Color is one of the most common ways to convey information in visualization applications. Color vision deficiency (CVD) affects approximately 200 million individuals worldwide and considerably degrades their performance in understanding such contents by creating red-green or blue-yellow ambiguities. While several content-specific methods have been proposed to resolve these ambiguities, they cannot achieve this effectively in many situations for contents with a large variety of colors. More importantly, they cannot facilitate color identification. We propose a technique for using patterns to encode color information for individuals with CVD, in particular for dichromats. We present the first content-independent method to overlay patterns on colored visualization contents that not only minimizes ambiguities but also allows color identification. Further, since overlaying patterns does not compromise the underlying original colors, it does not hamper the perception of normal trichromats. We validated our method with two user studies: one including 11 subjects with CVD and 19 normal trichromats, and focused on images that use colors to represent multiple categories; and another one including 16 subjects with CVD and 22 normal trichromats, which considered a broader set of images. Our results show that overlaying patterns significantly improves the performance of dichromats in several color-based visualization tasks, making their performance almost similar to normal trichromats'. More interestingly, the patterns augment color information in a positive manner, allowing normal trichromats to perform with greater accuracy.

The genetic combination of Hb Mobile (beta 73 Asp replaced by Val) and Hb S (beta 6 Glu replaced by Val) was found in a healthy black man whose hemolysate resembles that of Hb S electrophoretically. His mother and sister have Hb AS; the father and brother have Hb A Mobile. No clinical nor hematologic abnormalities were detected in any member of the family. A slightly decreased oxygen affinity associated with Hb Mobile appears to have no clinical significance. Simple methods of differentiating Hb Mobile S from the electrophoretically similar but clinically severe Hb SD Los Angeles are described.

The amino acid substitutions in two new hemoglobins found by electrophoretic screening during a survey in Alabama have been determined by column chromatography and amino acid analyses of their tryptic peptides. They are hemoglobin Alabama (beta 39(C 5)Gln leads to Lys) and hemoglobin Montgomery (alpha 48(CD 6) Leu leads to Arg). No harmful symptoms have been attributed to the presence of either hemoglobin.

Five new double-mutant haemoglobins composed of betaS chains and alpha chains with different substitutions, which are located at the surface of the tetramer, have been prepared. Although all the hybrids are more soluble than deoxyhaemoglobin S, the individual differences between these molecules make it possible to evaluate several regions on the alpha chains for intermolecular contacts in the polymerisation of deoxyhaemoglobin S.

Using a TRS-80 Radio Shack microcomputer system, we have computerized the differentiation of hemoglobin variants according to their mobilities in four methods of zone electrophoresis, each measuring a somewhat different aspect of molecular structure. In the identification routine of the program, the electrophoretic mobilities of an unknown variant are compared mathematically to the mobilities of previously analyzed variants; the computer prints out those known variants whose mobilities are within a specifiable interval on either side of the mobilities of the unknown variant. Properly specifying this interval is essential to the effectiveness of the identification. Another routine in the program classifies the variants according to any of ten molecular variables. Computerizing the identification and the information output provides a way to differentiate many variants, allows convenient handling of a large number of data on them, and facilitates their structural analysis.

By using a methylcellulose clonal assay, we cultured peripheral blood erythropoietic precursors (BFU-E) from an adult couple whose child had HbF Malta-I(gamma 117 His leads to Arg), a G gamma variant, and measured the synthetic rates of HbA, HbF, and HbF Malta-I. Hemoglobin was labeled with 14C-amino acid in culture, separated by slab gel isoelectric focusing technique, and quantitated by autoradiographic or fluorographic method. Culture of BFU-E from both parents revealed significant HbF biosynthesis. HbF Malta-I was present in culture of the father's cells and comprised about 24% of total HbF. When we analyzed Hb biosynthesis in individual bursts, all bursts contained HbA and HbF in varying ratios. The frequency distribution of the individual bursts differing in percentages of HbF biosynthesis approached normal distribution. While the relative ratio of HbF Malta-I to total HbF biosynthesis in individual bursts also revealed significant variation, its frequency distribution did not show a normal distribution. There was a positive correlation between the ratios of HbF/Hb and HbF Malta-I/HbF in individual bursts.

A new haemoglobin variant with a decreased oxygen affinity is described, in which the substitution, alpha 94 (G1) Asp replaced by Asn, affects the alpha1beta2 contact alpha1G1-beta2G4. The relevance of this variant to our understanding of the importance of the hydrogen bond between alpha1G1 and beta2G4 in Perutz's model of oxyhaemoglobin A is discussed.

A new hemoglobin variant found in a mother and her child was characterized by column chromatography of the tryptic hydrolysate of the aminoethylated, glycinamidated beta-chain, followed by chymotryptic digestion of the abnormal beta T-9 peptide and amino acid analyses. It was shown to be alpha2beta2 73(E17)Asp replaced by Val and named by Hb Mobile.

HbE, beta thalassemia, and G6PD deficiency were demonstrated in a 6-year-old Mexican-American child with anemia, jaundice, and delayed growth. The father was heterozygous for HbE, and the mother for beta-thalassemia and G6PD deficiency. The association of these three diseases should be included in the differential diagnosis of anemia in childhood, particularly after the recent influx of people form Southeast Asia into the United States.

The involvement of the COOH-terminal histidines of the beta chains of human hemoglobin in the allosteric mechanism of oxygen binding has been the topic of intensive discussion. Data presented here on the functional properties of native and chemically modified forms of Hb Cowtown (beta 146 His replaced by Leu) suggest that approximately half of the alkaline Bohr effect is attributable to the imidazole of His HC3(146) beta. The contribution of this residue to the alkaline Bohr effect has been estimated variably as 40-60% and 15% or less. Equilibrium and kinetic studies show that the amino acid substitution in Hb Cowtown decreases the stability of the low affinity conformation, resulting in an increased oxygen affinity and altered sensitivity to anionic effectors. Detailed analysis of Hill plots of oxygen binding according to the Adair scheme reveals that, under conditions of moderate ionic strength (chloride = 0.1 M), the K2 and K3 values for Hb A and Hb Cowtown differ, whereas the K1 and K4 values are closely similar over the physiological pH range. The decreased pH sensitivity of Hb Cowtown is associated with a decreased pH sensitivity of K1, the first Adair constant. In contrast to des-His(146 beta) hemoglobin, the cooperative interactions shown by Hb Cowtown under conditions of moderate ionic strength are not reduced in comparison to those of Hb A. This and the similarity of K1 and K4 values for Hb A and Hb Cowtown indicate that under these conditions the salt bridge formed by the COOH-terminal imidazole group does not significantly contribute to the free energy difference between "T-state" and "R-state" hemoglobin. It appears that the salt bridge formed by the COOH-terminal carboxyl group stabilizes the deoxy, T-state, conformation to a greater degree than previously appreciated. Chemical modification of the Cys(93 beta) residue of Hb Cowtown with N-ethylmaleimide causes a decrease in its oxygen affinity, in contrast to the increase in affinity exhibited by N-ethylmaleimide-modified Hb A. Hemoglobins A and Cowtown have remarkably similar oxygen binding properties after this modification and are shown to have K1 and K4 values distinctly different from those of unmodified Hb A. The properties of native and chemically modified forms of Hb Cowtown are indicative of a large contribution of the His HC3 (146) beta residue to the alkaline Bohr effect and also illustrate how chemical modifications or changes of strategic amino acid residues can result in pronounced differences in the conformational equilibrium of an allosteric protein.

Hemolysates of erythrocytes from more than a quarter million people in Alabama were electrophoresed on cellulose acetate, pH 8.4, and those samples exhibiting an abnormality were also electrophoresed in citrate agar, pH 6.0. The globin chains of mutants other than Hb S and C were electrophoresed in urea-mercaptoethanol buffers at both pH 8.9 and pH 6.0, and 60 of them were also analyzed structurally. Of about 6000 samples from whites, only three contained abnormal hemoglobins--Hb D Los Angeles, Hb J Baltimore, and one unidentified. Of 249,000 samples from blacks, about 29,000 contained electrophoretically detectable abnormalities, most of them associated with Hb S or C, present in a frequency of about 9% and 3%, respectively. About 1000 samples resolved into patterns of potential clinical significance. Twenty other mutant hemoglobins were detected, in various genetic combinations in 164 kindreds; four of these-Hb Alabama, Montgomery, Titusville, and Mobile--were previously unknown. The methods used are rapid, economical, and well suited for large scale surveys. They provide highly specific characterizations of many mutant hemoglobins, and no discrepancies were found between the presumptive identifications based on these characterizations and the definitive identifications obtained from structural analyses.

The presence of Hb New York was confirmed in a Chinese family in which affected members have occasional red cells with Hb-H-like inclusions and a relative decrease in alpha chain synthesis, suggestive of a coexisting alpha thalassaemia trait. However, globin gene mapping and DNA hybridization revealed no deletion of the alpha genome. Timed-incubation experiments showed that the rate of synthesis of beta NY chain was greater than that of normal beta chain in the early periods. Chromatographic separation of Hb NY and Hb A before chain analysis revealed preferential binding of newly synthesized alpha chains to beta NY, with a four-fold increase in specific activity of the alpha Hb NY chains. It is concluded that beta NY chain is being synthesized more rapidly and its increased turnover may account for this presentation of apparent alpha chain deficiency.

A system of calculating relative mobilities of mutant hemoglobins and globin chains in four methods of zone electrophoresis is described. In electrophoresis on cellulose acetate, TEB buffer, pH 8.5, mobilities are calculated as ratios of the mobility of simultaneously analyzed Hb C. In electrophoresis on citrate agar, pH 6.0, anodic mobilities are also related to Hb C, cathodic ones to Hb F. In globin electrophoresis in urea 2-mercaptoethanol buffers, pH 6.0 and 8.9, mobilities of the mutant globin chains are calculated in relation to the mobilities of normal alpha and beta chains. These calculations provide objective comparisons of mobilities of hemoglobins, including those analyzed at different times. The combined data permit recognition of many mutant hemoglobins.

Many mutant hemoglobins and hemoglobinopathies can be identified with a high degree of specificity in the routine clinical laboratory. The most frequent abnormalities--those involving Hb S or C--are usually easily detectable in small amounts of sample analyzed by two simple methods of electrophoresis: cellulose acetate at pH 8.5 and citrate agar at pH 6. Some rarer mutants, e.g., Hb O, Hope, and Camden, can also be recognized by these two methods. Presumptive identification of other relatively frequent mutants, such as Hb D Los Angeles (Punjab) and Hb G Philadelphia, can be accomplished with additional data obtained from globin electrophoresis on cellulose acetate in acidic and alkaline buffers containing urea and 2-mercaptoethanol (or dithioerythritol). Electrophoretic profiles are presented of about a dozen hemoglobins likely to be encountered in screening programs in the U.S. Methods are also presented for identifying other genetic hemoglobin abnormalities--various types of thalassemia, Hb M, unstable hemoglobins, and those of the newborn.

The comparative mobilities, in citrate agar electrophoresis, of 91 mutant hemoglobins are presented in relation to their molecular structure and in some cases, to their mobilities in other types of electrophoresis. More than a third of the alpha chain mutants (11 of the 27 examined) and half of the beta chain mutants (29 of 55) differ to some extent from Hb A. The helical location of the substituted residue is an important determinant of hemoglobin mobility, which is also affected by a complex interplay of other factors. When the data are combined with those of several other types of electrophoresis, they often provide presumptive (or in some cases highly specific) identifications of mutant hemoglobins and hemoglobinopathies.

Hemoglobin Ohio [beta 142 (H20) Ala replaced by Asp] was found in three members of a white family, all of whom showed erythrocytosis. The variant hemoglobin has a high oxygen affinity, a reduced Bohr effect, and diminished cooperativity. The functional abnormalities of Hb Ohio are explained by the proximity of the substituent beta 142 residue, both to beta 143 His, which is involved in the DPG binding site of hemoglobin, and to the critical C terminal region of the beta chain, which participates in the stabilization of the deoxy (T) conformation.

Hb Gun Hill has been found in an asymptomatic black female living in Alabama; neither her parents nor her two siblings carry the variant. The deletion of five amino acid residues in the beta chain of Hb Gun Hill (alpha2beta2 91-95 deleted) causes this variant to have a high oxygen affinity, an interaction coefficient of unity and an absence of the Bohr effect. The rate of oxidation of liganded Hb Gun Hill by the ferricyanide ion follows first-order kinetics. Hb Gun Hill is to a great extent dissociated into dimers over a wide range of pH values.

The amino acid substitution in a new hemoglobin variant, Hb Baylor (alpha2beta281 (EF5) Leu replaced by Arg), has been determined by application of column chromatography and amino acid analysis of the tryptic peptides. The hemoglobin is somewhat unstable and it has a high oxygen affinity. The propositus shows the opposing hematologic effects of these two properties--the instability being associated with increased destruction, and the high O2 affinity with increased production, of erythrocytes.

Hb Detroit is a mutant which migrates between Hb A and Hb J Baltimore on cellulose acetate (pH 8.5), and with Hb A on citrate agar (pH 6.0). Globin chain analyses in alkaline and acid buffers reveal an abnormal beta chain with a mobility between the betaA and betaJ Baltimore chains. Structural characterization of this abnormal chain shows that lysine at position 95 is replaced by asparagine. No hematological abnormalities could be attributed to the presence of the mutant, and the oxygen affinity properties of the stripped hemoglobin are similar to those of Hb A. The beta95 residue which is substituted in Hb Detroit and also in Hb N Baltimore ((beta95 Lys leads to Glu) does not appear to be in a critical functional area of the molecule.

A new mutant, hemoglobin Cowtown, has been found in a white man and his father, both of whom have erythrocytosis. The father had previously been treated with 32P for polycythemia vera. The abnormal hemoglobin is not detectable on electrophoresis in alkaline buffers, but it resolves distinctively on electrophoresis in citrate agar, pH 6.0; similarly, the abnormal beta-globin chain does not separate from beta-A in urea 2-mercaptoethanol buffers of pH 8.9, but it moves anodically to beta-A at pH 6.0. Peptide chromatography and amino acid analysis of the beta chain reveal that the C-terminal histidine residue (beta 146) has been replaced by leucine. Like several other hemoglobins substituted at this residue, Hb Cowtown has a high oxygen affinity and a diminished Bohr effect.

An abnormal fetal hemoglobin, designated hemoglobin F(Texas), was found in the cord blood of five Negro infants (all related and three of them siblings) and of one Caucasian infant. Studies on the chemical structure of this variant indicate that there is a substitution of a lysyl residue for either the fifth or sixth glutamyl residue of the gamma-chain.